A Critical Test of the Electrostatic Contribution to Catalysis with Noncanonical Amino Acids in Ketosteroid Isomerase

Noncanonical Amino Acids in Biocatalysis

In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.

Non-canonical amino acids uncover the significant impact of Tyr671 on Taq DNA polymerase catalytic activity

Responsible for synthesizing the complementary strand of the DNA template, DNA polymerase is a crucial enzyme in DNA replication, recombination and repair. A highly conserved tyrosine (Tyr), located at the C-terminus of the O-helix in family A DNA polymerases, plays a critical role in enzyme activity and fidelity. Here, we combined the technology of genetic code extension to incorporate non-canonical amino acids and molecular dynamics (MD) simulations to uncover the mechanisms by which Tyr671 impacts substrate binding and conformation transitions in a DNA polymerase from Thermus aquaticus. Five non-canonical amino acids, namely l-3,4-dihydroxyphenylalanine (l-DOPA), p-aminophenylalanine (pAF), p-acetylphenylalanine (pAcF), p-cyanophenylalanine (pCNF) and p-nitrophenylalanine (pNTF), were individually incorporated at position 671. Strikingly, Y671pAF and Y671DOPA were active, but with lower activity compared to Y671F and wild-type. Y671pAF showed a higher fidelity than the Y671F, despite both possessing lower fidelity than the wild-type. Metadynamics and long-timescale MD simulations were carried out to probe the role of mutations in affecting protein structure, including open conformation, open-to-closed conformation transition, closed conformation, and closed-to-open conformation transition. The MD simulations clearly revealed that the size of the 671 amino acid residue and interactions with substrate or nearby residues were critical for Tyr671 to determine enzyme activity and fidelity.

Directed Evolution of Protoglobin Optimizes the Enzyme Electric Field

To unravel why computational design fails in creating viable enzymes, while directed evolution (DE) succeeds, our research delves into the laboratory evolution of protoglobin. DE has adapted this protein to efficiently catalyze carbene transfer reactions. We show that the previously proposed enhanced substrate access and binding alone cannot account for increased yields during DE. The 3D electric field in the entire active site is tracked through protein dynamics, clustered using the affinity propagation algorithm, and subjected to principal component analysis. This analysis reveals notable changes in the electric field with DE, where distinct field topologies influence transition state energetics and mechanism. A chemically meaningful field component emerges and takes the lead during DE and facilitates crossing the barrier to carbene transfer. Our findings underscore intrinsic electric field dynamic's influence on enzyme function, the ability of the field to switch mechanisms within the same protein, and the crucial role of the field in enzyme design.

Long-range electrostatic effects from intramolecular Lewis acid binding influence the redox properties of cobalt-porphyrin complexes

A CoII-porphyrin complex (1) with an appended aza-crown ether for Lewis acid (LA) binding was synthesized and characterized. NMR spectroscopy and electrochemistry show that cationic group I and II LAs (i.e., Li+, Na+, K+, Ca2+, Sr2+, and Ba2+) bind to the aza-crown ether group of 1. The binding constant for Li+ is comparable to that observed for a free aza-crown ether. LA binding causes an anodic shift in the CoII/CoI couple of between 10 and 40 mV and also impacts the CoIII/CoII couple. The magnitude of the anodic shift of the CoII/CoI couple varies linearly with the strength of the LA as determined by the pKa of the corresponding metal-aqua complex, with dications giving larger shifts than monocations. The extent of the anodic shift of the CoII/CoI couple also increases as the ionic strength of the solution decreases. This is consistent with electric field effects being responsible for the changes in the redox properties of 1 upon LA binding and provides a novel method to tune the reduction potential. Density functional theory calculations indicate that the bound LA is 5.6 to 6.8 Å away from the CoII ion, demonstrating that long-range electrostatic effects, which do not involve changes to the primary coordination sphere, are responsible for the variations in redox chemistry. Compound 1 was investigated as a CO2 reduction electrocatalyst and shows high activity but rapid decomposition.

Critical Evaluation of Polarizable and Nonpolarizable Force Fields for Proteins Using Experimentally Derived Nitrile Electric Fields

Molecular dynamics (MD) simulations are frequently carried out for proteins to investigate the role of electrostatics in their biological function. The choice of force field (FF) can significantly alter the MD results, as the simulated local electrostatic interactions lack benchmarking in the absence of appropriate experimental methods. We recently reported that the transition dipole moment (TDM) of the popular nitrile vibrational probe varies linearly with the environmental electric field, overcoming well-known hydrogen bonding (H-bonding) issues for the nitrile frequency and, thus, enabling the unambiguous measurement of electric fields in proteins (J. Am. Chem. Soc. 2022, 144 (17), 7562-7567). Herein, we utilize this new strategy to enable comparisons of experimental and simulated electric fields in protein environments. Specifically, previously determined TDM electric fields exerted onto nitrile-containing o-cyanophenylalanine residues in photoactive yellow protein are compared with MD electric fields from the fixed-charge AMBER FF and the polarizable AMOEBA FF. We observe that the electric field distributions for H-bonding nitriles are substantially affected by the choice of FF. As such, AMBER underestimates electric fields for nitriles experiencing moderate field strengths; in contrast, AMOEBA robustly recapitulates the TDM electric fields. The FF dependence of the electric fields can be partly explained by the presence of additional negative charge density along the nitrile bond axis in AMOEBA, which is due to the inclusion of higher-order multipole parameters; this, in turn, begets more head-on nitrile H-bonds. We conclude by discussing the implications of the FF dependence for the simulation of nitriles and proteins in general.

Electrostatics as a Guiding Principle in Understanding and Designing Enzymes

Enzyme design faces challenges related to the implementation of the basic principles that govern the catalytic activity in natural enzymes. In this work, we revisit basic electrostatic concepts that have been shown to explain the origin of enzymatic efficiency like preorganization and reorganization. Using magnitudes such as the electrostatic potential and the electric field generated by the protein, we explain how these concepts work in different enzymes and how they can be used to rationalize the consequences of point mutations. We also discuss examples of protein design in which electrostatic effects have been implemented. For the near future, molecular simulations, coupled with the use of machine learning methods, can be used to implement electrostatics as a guiding principle for enzyme designs.

Hydrophobicity-Based Force Field In Enzymes

The biocatalysis process takes place with the participation of enzymes, which, depending on the reaction carried out, require, apart from the appropriate arrangement of catalytic residues, an appropriate external force field. It is generated by the protein body. The relatively small size of the part directly involved in the process itself is supported by the presence of an often complex structure of the protein body, the purpose of which is to provide an appropriate local force field, eliminating the influence of water. Very often, the large size of the enzyme is an expression of the complex form of this field. In this paper, a comparative analysis of arbitrarily selected enzymes, representatives of different enzyme classes, was carried out, focusing on the measurement of the diversity of the force field provided by a given protein. This analysis was based on the fuzzy oil drop model (FOD) and its modified version (FOD-M), which takes into account the participation of nonaqueous external factors in shaping the structure and thus the force field within the protein. The degree and type of ordering of the hydrophobicity distribution in the protein molecule is the result of the influence of the environment but also the supplier of the local environment for a given process, including the catalysis process in particular. Determining the share of a nonaqueous environment is important due to the ubiquity of polar water, whose participation in processes with high specificity requires control. It can be assumed that some enzymes in their composition have a permanently built-in part, the role of which is reduced to that of a permanent chaperone. It provides a specific external force field needed for the process. The proposed model, generalized to other types of proteins, may also provide a form of recording the environment model for the simulation of the in silico protein folding process, taking into account the impact of its differentiation.

Theoretical Improvements in Enzyme Efficiency Associated with Noisy Rate Constants and Increased Dissipation

Previous studies have revealed the extraordinarily large catalytic efficiency of some enzymes. High catalytic proficiency is an essential accomplishment of biological evolution. Natural selection led to the increased turnover number, kcat, and enzyme efficiency, kcat/KM, of uni-uni enzymes, which convert a single substrate into a single product. We added or multiplied random noise with chosen rate constants to explore the correlation between dissipation and catalytic efficiency for ten enzymes: beta-galactosidase, glucose isomerase, β-lactamases from three bacterial strains, ketosteroid isomerase, triosephosphate isomerase, and carbonic anhydrase I, II, and T200H. Our results highlight the role of biological evolution in accelerating thermodynamic evolution. The catalytic performance of these enzymes is proportional to overall entropy production-the main parameter from irreversible thermodynamics. That parameter is also proportional to the evolutionary distance of β-lactamases PC1, RTEM, and Lac-1 when natural or artificial evolution produces the optimal or maximal possible catalytic efficiency. De novo enzyme design and attempts to speed up the rate-limiting catalytic steps may profit from the described connection between kinetics and thermodynamics.

Studying Local Electrostatics by Terahertz Spectroscopy Using Amines as a Probe

In a previous study[1] we could show that a large amplitude mode of the zwitterion glycine can serve as a sensitive probe for protonation and allows to deduce local pKa values. Here we show that the underlying concept is more general: We present the results of a pH dependent measurement of Terahertz-FTIR (THz-FTIR) spectra of solvated amines, i. e. Diethylamine (DEA), Triethylamine (TEA), and Diisopropylamine (DiPA). We show that amines serve as a sensitive, label free probe for local protonation. Protonation of the amines yield intensity changes which can be quantified by precise THz spectroscopy (30 cm-1 -450 cm-1 ). A detailed analysis allows us to correlate the titration spectra of solvated amines in the THz range with pKa values. This demonstrates the potential of THz spectroscopy to probe the charge state of biomolecules in water in a label free manner.

Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions

In enzyme mechanistic studies and mutant design, it is highly desirable to know the individual residue contributions to the reaction free energy and barrier. In this work, we show that such free energy contributions from each residue can be readily obtained by postprocessing ab initio quantum mechanical molecular mechanical (ai-QM/MM) free energy simulation trajectories. Specifically, through a mean force integration along the minimum free energy pathway, one can obtain the electrostatic, polarization, and van der Waals contributions from each residue to the free energy barrier. Separately, a similar analysis procedure allows us to assess the contribution from different collective variables along the reaction coordinate. The chorismate mutase reaction is used to demonstrate the utilization of these two trajectory analysis tools.

High Electric Fields on Water Microdroplets Catalyze Spontaneous and Fast Reactions in Halogen-Bond Complexes

The use of external electric fields as green and efficient catalysts in synthetic chemistry has recently received significant attention for their ability to deliver remarkable control of reaction selectivity and acceleration of reaction rates. Technically, methods of generating high electric fields in the range of 1-10 V/nm are limited, as in-vacuo techniques have obvious scalability issues. The spontaneous high fields at various interfaces promise to solve this problem. In this study, we take advantage of the spontaneous high electric field at the air-water interface of sprayed water microdroplets in the reactions of several halogen bond systems: Nu:--X-X, where Nu: is pyridine or quinuclidine and X is bromine or iodine. The field facilitates ultrafast electron transfer from Nu:, yielding a Nu-X covalent bond and causing the X-X bond to cleave. This reaction occurs in microseconds in microdroplets but takes days to weeks in bulk solution. Density functional theory calculations predict that the reaction becomes barrier-free in the presence of oriented external electric fields, supporting the notion that the electric fields in the water droplets are responsible for the catalysis. We anticipate that microdroplet chemistry will be an avenue rich in opportunities in the reactions facilitated by high electric fields and provides an alternative way to tackle the scalability problem.

Evaluating the Transition State Stabilization/Destabilization Effects of the Electric Fields from Scaffold Residues by a QM/MM Approach

The protein scaffolds of enzymes not only provide structural support for the catalytic center but also exert preorganized electric fields for electrostatic catalysis. In recent years, uniform oriented external electric fields (OEEFs) have been widely applied to enzymatic reactions to mimic the electrostatic effects of the environment. However, the electric fields exerted by individual residues in proteins may be quite heterogeneous across the active site, with varying directions and strengths at different positions of the active site. Here, we propose a QM/MM-based approach to evaluate the effects of the electric fields exerted by individual residues in the protein scaffold. In particular, the heterogeneity of the residue electric fields and the effect of the native protein environment can be properly accounted for by this QM/MM approach. A case study of the O-O heterolysis reaction in the catalytic cycle of TyrH shows that (1) for scaffold residues that are relatively far from the active site, the heterogeneity of the residue electric field in the active site is not very significant and the electrostatic stabilization/destabilization due to each residue can be well approximated with the interaction energy between a uniform electric field and the QM region dipole; (2) for scaffold residues near the active site, the residue electric fields can be highly heterogeneous along the breaking O-O bond. In such a case, approximating the residue electric fields as uniform fields may misrepresent the overall electrostatic effect of the residue. The present QM/MM approach can be applied to evaluate the residues' electrostatic impact on enzymatic reactions, which also can be useful in computational optimization of electric fields to boost the enzyme catalysis.

Engineering mutually orthogonal PylRS/tRNA pairs for dual encoding of functional histidine analogues

The availability of an expanded genetic code opens exciting new opportunities in enzyme design and engineering. In this regard histidine analogues have proven particularly versatile, serving as ligands to augment metalloenzyme function and as catalytic nucleophiles in designed enzymes. The ability to genetically encode multiple functional residues could greatly expand the range of chemistry accessible within enzyme active sites. Here, we develop mutually orthogonal translation components to selectively encode two structurally similar histidine analogues. Transplanting known mutations from a promiscuous Methanosarcina mazei pyrrolysyl-tRNA synthetase (MmPylRSIFGFF ) into a single domain PylRS from Methanomethylophilus alvus (MaPylRSIFGFF ) provided a variant with improved efficiency and specificity for 3-methyl-L-histidine (MeHis) incorporation. The MaPylRSIFGFF clone was further characterized using in vitro biochemical assays and x-ray crystallography. We subsequently engineered the orthogonal MmPylRS for activity and selectivity for 3-(3-pyridyl)-L-alanine (3-Pyr), which was used in combination with MaPylRSIFGFF to produce proteins containing both 3-Pyr and MeHis. Given the versatile roles played by histidine in enzyme mechanisms, we anticipate that the tools developed within this study will underpin the development of enzymes with new and enhanced functions.

Protein Dynamics and Enzymatic Catalysis

This Perspective presents a review of our work and that of others in the highly controversial topic of the coupling of protein dynamics to reaction in enzymes. We have been involved in studying this topic for many years. Thus, this perspective will naturally present our own views, but it also is designed to present an overview of the variety of viewpoints of this topic, both experimental and theoretical. This is obviously a large and contentious topic.

Geometry of Charge Density as a Reporter on the Role of the Protein Scaffold in Enzymatic Catalysis: Electrostatic Preorganization and Beyond

Enzymes host active sites inside protein macromolecules, which have diverse, often incredibly complex, and atom-expensive structures. It is an outstanding question what the role of these expensive scaffolds might be in enzymatic catalysis. Answering this question is essential to both enzymology and the design of artificial enzymes with proficiencies that will match those of the best natural enzymes. Protein rigidifying the active site, contrasted with the dynamics and vibrational motion promoting the reaction, as well as long-range electrostatics (also known as electrostatic preorganization) were all proposed as central contributions of the scaffold to the catalysis. Here, we show that all these effects inevitably produce changes in the quantum mechanical electron density in the active site, which in turn defines the reactivity. The phenomena are therefore fundamentally inseparable. The geometry of the electron density-a scalar field characterized by a number of mathematical features such as critical points-is a rigorous and convenient descriptor of enzymatic catalysis and a reporter on the role of the protein. We show how this geometry can be analyzed, linked to the reaction barriers, and report in particular on intramolecular electric fields in enzymes. We illustrate these tools on the studies of electrostatic preorganization in several representative enzyme classes, both natural and artificial. We highlight the forward-looking aspects of the approach.

Automated Variable Electric-Field DFT Application for Evaluation of Optimally Oriented Electric Fields on Chemical Reactivity

Recent theoretical work and experiments at molecular junctions have provided a strong conceptualization for the effects of oriented electric fields (OEFs) on organic reactions. Depending on the axis of application, OEFs can increase (or decrease) the reaction rate or distinguish between isomeric pathways. Despite the conceptual elegance of OEFs, which may be applied externally or induced locally, as tools for catalyzing organic reactions, implementation in synthetically relevant systems has been hampered by inefficiencies in evaluating reaction sensitivity to field effects. Herein, we describe the development of the Automated Variable Electric-Field DFT Application (A.V.E.D.A.) for streamlined evaluation of a reaction's susceptibility to OEFs. This open-source software was designed to be accessible for nonexpert users of computational and programming tools. Following initiation by a single command (and with no subsequent intervention) the Linux workflow manages a series of density functional theory calculations and mathematical manipulations to optimize local-minimum and transition-state structures in oriented electric fields of increasing magnitude. The resulting molecular and reaction dipole moments, field-perturbed geometries, and net effective activation energies are compiled for user interpretation. Ten representative pericyclic reactions that showcase the development and evaluation of A.V.E.D.A. are described.

Setting Boundaries for Statistical Mechanics

Statistical mechanics has grown without bounds in space. Statistical mechanics of noninteracting point particles in an unbounded perfect gas is widely used to describe liquids like concentrated salt solutions of life and electrochemical technology, including batteries. Liquids are filled with interacting molecules. A perfect gas is a poor model of a liquid. Statistical mechanics without spatial bounds is impossible as well as imperfect, if molecules interact as charged particles, as nearly all atoms do. The behavior of charged particles is not defined until boundary structures and values are defined because charges are governed by Maxwell's partial differential equations. Partial differential equations require boundary structures and conditions. Boundary conditions cannot be defined uniquely 'at infinity' because the limiting process that defines 'infinity' includes such a wide variety of structures and behaviors, from elongated ellipses to circles, from light waves that never decay, to dipolar fields that decay steeply, to Coulomb fields that hardly decay at all. Boundaries and boundary conditions needed to describe matter are not prominent in classical statistical mechanics. Statistical mechanics of bounded systems is described in the EnVarA system of variational mechanics developed by Chun Liu, more than anyone else. EnVarA treatment does not yet include Maxwell equations.

Engineering enzyme activity using an expanded amino acid alphabet

Enzyme design and engineering strategies are typically constrained by the limited size of nature's genetic alphabet, comprised of only 20 canonical amino acids. In recent years, site-selective incorporation of non-canonical amino acids (ncAAs) via an expanded genetic code has emerged as a powerful means of inserting new functional components into proteins, with hundreds of structurally diverse ncAAs now available. Here, we highlight how the emergence of an expanded repertoire of amino acids has opened new avenues in enzyme design and engineering. ncAAs have been used to probe complex biological mechanisms, augment enzyme function and, most ambitiously, embed new catalytic mechanisms into protein active sites that would be challenging to access within the constraints of nature's genetic code. We predict that the studies reviewed in this article, along with further advances in genetic code expansion technology, will establish ncAA incorporation as an increasingly important tool for biocatalysis in the coming years.

Perspective: Path Sampling Methods Applied to Enzymatic Catalysis

This Perspective reviews the use of Transition Path Sampling methods to study enzymatically catalyzed chemical reactions. First applied by our group to an enzymatic reaction over 15 years ago, the method has uncovered basic principles in enzymatic catalysis such as the protein promoting vibration, and it has also helped harmonize such ideas as electrostatic preorganization with dynamic views of enzyme function. It is now being used to help uncover principles of protein design necessary to artificial enzyme creation.

TUPÃ: Electric field analyses for molecular simulations

We introduce TUPÃ, a Python-based algorithm to calculate and analyze electric fields in molecular simulations. To demonstrate the features in TUPÃ, we present three test cases in which the orientation and magnitude of the electric field exerted by biomolecules help explain biological phenomena or observed kinetics. As part of TUPÃ, we also provide a PyMOL plugin to help researchers visualize how electric fields are organized within the simulation system. The code is freely available and can be obtained at https://mdpoleto.github.io/tupa/.

The road to fully programmable protein catalysis

The ability to design efficient enzymes from scratch would have a profound effect on chemistry, biotechnology and medicine. Rapid progress in protein engineering over the past decade makes us optimistic that this ambition is within reach. The development of artificial enzymes containing metal cofactors and noncanonical organocatalytic groups shows how protein structure can be optimized to harness the reactivity of nonproteinogenic elements. In parallel, computational methods have been used to design protein catalysts for diverse reactions on the basis of fundamental principles of transition state stabilization. Although the activities of designed catalysts have been quite low, extensive laboratory evolution has been used to generate efficient enzymes. Structural analysis of these systems has revealed the high degree of precision that will be needed to design catalysts with greater activity. To this end, emerging protein design methods, including deep learning, hold particular promise for improving model accuracy. Here we take stock of key developments in the field and highlight new opportunities for innovation that should allow us to transition beyond the current state of the art and enable the robust design of biocatalysts to address societal needs.

Influence of an Oriented External Electric Field on the Mechanism of Double Proton Transfer between Pyrazole and Guanidine: from an Asynchronous Plateau Transition State to a Synchronous or Stepwise Mechanism

The double proton transfer (DPT) reaction between pyrazole and guanidine, a concerted reaction but strongly asynchronous and presenting a "plateau transition region", has been theoretically reinvestigated in the presence of an external uniform electric field. First, we computed the reaction path by DFT and proposed a very detailed description of the constitutive electronic events, based on the ELF topology and the bond evolution theory. Then, we studied the effect of an oriented external electric field (OEEF) on the reaction mechanism, for an OEEF oriented along the proton transfer axis. We observe that in one direction, the DPT reaction can be transformed into a stepwise reaction, going through a stabilized single proton transferred intermediate. Contrarily, the two proton transfers occur simultaneously when the electric field is applied in the opposite direction. In the latter case, the order in which the two protons are transferred in the same elementary step can even be reversed if the OEEF is intense enough. Finally, it has been shown that the evolution of the double proton transfer reaction in the presence of an electric field could be quantitatively anticipated by analyzing the ELF value at the bifurcation point between V(A, H) proton donor and V(B) proton acceptor of the double hydrogen bonded complex in the entrance channel.

A two-directional vibrational probe reveals different electric field orientations in solution and an enzyme active site

The catalytic power of an electric field depends on its magnitude and orientation with respect to the reactive chemical species. Understanding and designing new catalysts for electrostatic catalysis thus requires methods to measure the electric field orientation and magnitude at the molecular scale. We demonstrate that electric field orientations can be extracted using a two-directional vibrational probe by exploiting the vibrational Stark effect of both the C=O and C-D stretches of a deuterated aldehyde. Combining spectroscopy with molecular dynamics and electronic structure partitioning methods, we demonstrate that, despite distinct polarities, solvents act similarly in their preference for electrostatically stabilizing large bond dipoles at the expense of destabilizing small ones. In contrast, we find that for an active-site aldehyde inhibitor of liver alcohol dehydrogenase, the electric field orientation deviates markedly from that found in solvents, which provides direct evidence for the fundamental difference between the electrostatic environment of solvents and that of a preorganized enzyme active site.

Molecular Dynamics-Derived Descriptor Informs the Impact of Mutation on the Catalytic Turnover Number in Lactonase Across Substrates

Molecular dynamics simulations have been extensively employed to reveal the roles of protein dynamics in mediating enzyme catalysis. However, simulation-derived predictive descriptors that inform the impacts of mutations on catalytic turnover numbers remain largely unexplored. In this work, we report the identification of molecular modeling-derived descriptors to predict mutation effect on the turnover number of lactonase SsoPox with both native and non-native substrates. The study consists of 10 enzyme-substrate complexes resulting from a combination of five enzyme variants with two substrates. For each complex, we derived 15 descriptors from molecular dynamics simulations and applied principal component analysis to rank the predictive capability of the descriptors. A top-ranked descriptor was identified, which is the solvent-accessible surface area (SASA) ratio of the substrate to the active site pocket. A uniform volcano-shaped plot was observed in the distribution of experimental activation free energy against the SASA ratio. To achieve efficient lactonase hydrolysis, a non-native substrate-bound enzyme variant needs to involve a similar range of the SASA ratio to the native substrate-bound wild-type enzyme. The descriptor reflects how well the enzyme active site pocket accommodates a substrate for reaction, which has the potential of guiding optimization of enzyme reaction turnover for non-native chemical transformations.

Integration of Experimental Data and Use of Automated Fitting Methods in Developing Protein Force Fields

The development of accurate protein force fields has been the cornerstone of molecular simulations for the past 50 years. During this period, many lessons have been learned regarding the use of experimental target data and parameter fitting procedures. Here, we review recent advances in protein force field development. We discuss the recent emergence of polarizable force fields and the role of electronic polarization and areas in which additive force fields fall short. The use of automated fitting methods and the inclusion of additional experimental solution data during parametrization is discussed as a means to highlight possible routes to improve the accuracy of force fields even further.

Energetic Basis and Design of Enzyme Function Demonstrated Using GFP, an Excited-State Enzyme

The past decades have witnessed an explosion of de novo protein designs with a remarkable range of scaffolds. It remains challenging, however, to design catalytic functions that are competitive with naturally occurring counterparts as well as biomimetic or nonbiological catalysts. Although directed evolution often offers efficient solutions, the fitness landscape remains opaque. Green fluorescent protein (GFP), which has revolutionized biological imaging and assays, is one of the most redesigned proteins. While not an enzyme in the conventional sense, GFPs feature competing excited-state decay pathways with the same steric and electrostatic origins as conventional ground-state catalysts, and they exert exquisite control over multiple reaction outcomes through the same principles. Thus, GFP is an "excited-state enzyme". Herein we show that rationally designed mutants and hybrids that contain environmental mutations and substituted chromophores provide the basis for a quantitative model and prediction that describes the influence of sterics and electrostatics on excited-state catalysis of GFPs. As both perturbations can selectively bias photoisomerization pathways, GFPs with fluorescence quantum yields (FQYs) and photoswitching characteristics tailored for specific applications could be predicted and then demonstrated. The underlying energetic landscape, readily accessible via spectroscopy for GFPs, offers an important missing link in the design of protein function that is generalizable to catalyst design.

Non-canonical Amino Acid Substrates of E. coli Aminoacyl-tRNA Synthetases

In this comprehensive review, I focus on the twenty E. coli aminoacyl-tRNA synthetases and their ability to charge non-canonical amino acids (ncAAs) onto tRNAs. The promiscuity of these enzymes has been harnessed for diverse applications including understanding and engineering of protein function, creation of organisms with an expanded genetic code, and the synthesis of diverse peptide libraries for drug discovery. The review catalogues the structures of all known ncAA substrates for each of the 20 E. coli aminoacyl-tRNA synthetases, including ncAA substrates for engineered versions of these enzymes. Drawing from the structures in the list, I highlight trends and novel opportunities for further exploitation of these ncAAs in the engineering of protein function, synthetic biology, and in drug discovery.

Key difference between transition state stabilization and ground state destabilization: increasing atomic charge densities before or during enzyme–substrate binding

The origin of the enormous catalytic power of enzymes has been extensively studied through experimental and computational approaches. Although precise mechanisms are still subject to much debate, enzymes are thought to catalyze reactions by stabilizing transition states (TSs) or destabilizing ground states (GSs). By exploring the catalysis of various types of enzyme–substrate noncovalent interactions, we found that catalysis by TS stabilization and the catalysis by GS destabilization share common features by reducing the free energy barriers (ΔG^‡s) of reactions, but are different in attaining the requirement for ΔG^‡ reduction. Irrespective of whether enzymes catalyze reactions by TS stabilization or GS destabilization, they reduce ΔG^‡s by enhancing the charge densities of catalytic atoms that experience a reduction in charge density between GSs and TSs. Notably, in TS stabilization, the charge density of catalytic atoms is enhanced prior to enzyme–substrate binding; whereas in GS destabilization, the charge density of catalytic atoms is enhanced during the enzyme–substrate binding. Results show that TS stabilization and GS destabilization are not contradictory to each other and are consistent in reducing the ΔG^‡s of reactions. The full mechanism of enzyme catalysis includes the mechanism of reducing ΔG^‡ and the mechanism of enhancing atomic charge densities. Our findings may help resolve the debate between TS stabilization and GS destabilization and assist our understanding of catalysis and the design of artificial enzymes.

Transition state stabilization and ground state destabilization utilize the same molecular mechanism when lowering the free energy barriers (ΔG^‡s) of reactions, but differ in achieving the requirement for ΔG^‡ reduction.

Electron Density Geometry and the Quantum Theory of Atoms in Molecules

A novel form of charge density analysis, that of isosurface curvature redistribution, is formulated and applied to the toy problem of carbonyl oxygen activation in formaldehyde. The isosurface representation of the electron charge density allows us to incorporate the rigorous geometric constraints of closed surfaces toward the analysis and chemical interpretation of the charge density response to perturbations. Visual inspection of 2D isosurface motion resulting from applied external electric fields reveals how the isosurface curvature flows within and between atoms and that a molecule can be uniquely and completely partitioned into chemically significant regions of positive and negative curvatures. These concepts reveal that carbonyl oxygen activation proceeds primarily through curvature and charge redistribution within rather than between Bader atoms. Using gradient bundle analysis─the partitioning of formaldehyde into infinitesimal volume elements bounded by QTAIM zero-flux surfaces─the observations from visual isosurface inspection are verified. The results of the formaldehyde carbonyl analysis are then shown to be transferable to the substrate carbonyl in the ketosteroid isomerase enzyme, laying the groundwork for extending this approach to the problems of enzymatic catalysis.

The Interplay of Electrostatics and Chemical Positioning in the Evolution of Antibiotic Resistance in TEM β-Lactamases

The interplay of enzyme active site electrostatics and chemical positioning is important for understanding the origin(s) of enzyme catalysis and the design of novel catalysts. We reconstruct the evolutionary trajectory of TEM-1 β-lactamase to TEM-52 toward extended-spectrum activity to better understand the emergence of antibiotic resistance and to provide insights into the structure-function paradigm and noncovalent interactions involved in catalysis. Utilizing a detailed kinetic analysis and the vibrational Stark effect, we quantify the changes in rates and electric fields in the Michaelis and acyl-enzyme complexes for penicillin G and cefotaxime to ascertain the evolutionary role of electric fields to modulate function. These data are combined with MD simulations to interpret and quantify the substrate-dependent structural changes during evolution. We observe that this evolutionary trajectory utilizes a large preorganized electric field and substrate-dependent chemical positioning to facilitate catalysis. This governs the evolvability, substrate promiscuity, and protein fitness landscape in TEM β-lactamase antibiotic resistance.

Engineering Translation Components for Genetic Code Expansion

The expansion of the genetic code consisting of four bases and 20 amino acids into diverse building blocks has been an exciting topic in synthetic biology. Many biochemical components are involved in gene expression; therefore, adding a new component to the genetic code requires engineering many other components that interact with it. Genetic code expansion has advanced significantly for the last two decades with the engineering of several components involved in protein synthesis. These components include tRNA/aminoacyl-tRNA synthetase, new codons, ribosomes, and elongation factor Tu. In addition, biosynthesis and enhanced uptake of non-canonical amino acids have been attempted and have made meaningful progress. This review discusses the efforts to engineer these translation components, to improve the genetic code expansion technology.

Globally Optimized Molecular Embeddings for Dynamic Reaction Solvate Shell Optimization and Active Site Design

We demonstrate how a full QM/MM derivatization of the recently developed GOCAT model can be utilized in the global optimization of molecular embeddings. To this end, we provide two distinct examples: An $$\text {S}_\text {N}2$$ S N 2 reaction, and one enzymatic example of recent interest, the ketosteroid isomerase. These serve us to highlight the advantages of such an approach and sketch the roadmap for further improvements.

Local Electric Fields in Aqueous Electrolytes

Vibrational Stark shifts were explored in aqueous solutions of organic molecules with carbonyl- and nitrile-containing constituents. In many cases, the vibrational resonances from these moieties shifted toward lower frequency as salt was introduced into solution. This is in contrast to the blue-shift that would be expected based upon Onsager's reaction field theory. Salts containing well-hydrated cations like Mg²⁺ or Li⁺ led to the most pronounced Stark shift for the carbonyl group, while poorly hydrated cations like Cs⁺ had the greatest impact on nitriles. Moreover, salts containing I^- gave rise to larger Stark shifts than those containing Cl^-. Molecular dynamics simulations indicated that cations and anions both accumulate around the probe in an ion- and probe-dependent manner. An electric field was generated by the ion pair, which pointed from the cation to the anion through the vibrational chromophore. This resulted from solvent-shared binding of the ions to the probes, consistent with their positions in the Hofmeister series. The "anti-Onsager" Stark shifts occur in both vibrational spectroscopy and fluorescence measurements.

Structural Basis for Isomerization Reactions in Fungal Tetrahydroxanthone Biosynthesis and Diversification

The novel isomerase NsrQ, from Aspergillus novofumigatus, is a key enzyme in the biosynthesis of fungal tetrahydroxanthones and is responsible for dearomatizing cyclization to provide a tetrahydroxanthone scaffold. NsrQ catalyzes a two-step isomerization reaction, involving the isomerization of allylic alcohol and subsequent inversion of configuration at the methyl group. We report on the biochemical and structural characterizations of NsrQ, and its homologue Dcr3, from Diaporthe longicolla. The crystal structures of NsrQ and Dcr3 revealed their similar overall structures, with a cone-shaped α+β barrel fold, to those of the nuclear transport factor 2-like superfamily enzymes. Furthermore, the structures of Dcr3 and NsrQ variants complexed with substrate analogues and the site-directed mutagenesis studies identified the catalytic residues and the important hydrophobic residues in shaping the active site pocket for substrate binding. These enzymes thus utilize Glu and His residues as acid-base catalysts. Based on these observations, we proposed a detailed reaction mechanism for NsrQ-catalyzed isomerization reactions.

Testing the Limitations of MD-Based Local Electric Fields Using the Vibrational Stark Effect in Solution: Penicillin G as a Test Case

Noncovalent interactions underlie nearly all molecular processes in the condensed phase from solvation to catalysis. Their quantification within a physically consistent framework remains challenging. Experimental vibrational Stark effect (VSE)-based solvatochromism can be combined with molecular dynamics (MD) simulations to quantify the electrostatic forces in solute-solvent interactions for small rigid molecules and, by extension, when these solutes bind in enzyme active sites. While generalizing this approach toward more complex (bio)molecules, such as the conformationally flexible and charged penicillin G (PenG), we were surprised to observe inconsistencies in MD-based electric fields. Combining synthesis, VSE spectroscopy, and computational methods, we provide an intimate view on the origins of these discrepancies. We observe that the electric fields are correlated to conformation-dependent effects of the flexible PenG side chain, including both the local solvation structure and solute conformational sampling in MD. Additionally, we identified that MD-based electric fields are consistently overestimated in three-point water models in the vicinity of charged groups; this cannot be entirely ameliorated using polarizable force fields (AMOEBA) or advanced water models. This work demonstrates the value of the VSE as a direct method for experiment-guided refinements of MD force fields and establishes a general reductionist approach to calibrating vibrational probes for complex (bio)molecules.

Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet

The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.

An electrostatic energy-based charge model for molecular dynamics simulation

The interactions of the polar chemical bonds such as C=O and N-H with an external electric field were investigated, and a linear relationship between the QM/MM interaction energies and the electric field along the chemical bond is established in the range of weak to intermediate electrical fields. The linear relationship indicates that the electrostatic interactions of a polar group with its surroundings can be described by a simple model of a dipole with constant moment under the action of an electric field. This relationship is employed to develop a general approach to generating an electrostatic energy-based charge (EEC) model for molecules containing single or multiple polar chemical bonds. Benchmark test studies of this model were carried out for (CH₃)₂-CO and N-methyl acetamide in explicit water, and the result shows that the EEC model gives more accurate electrostatic energies than those given by the widely used charge model based on fitting to the electrostatic potential (ESP) in direct comparison to the energies computed by the QM/MM method. The MD simulations of the electric field at the active site of ketosteroid isomerase based on EEC demonstrated that EEC gave a better representation of the electrostatic interaction in the hydrogen-bonding environment than the Amber14SB force field by comparison with experiment. The current study suggests that EEC should be better suited for molecular dynamics study of molecular systems with polar chemical bonds such as biomolecules than the widely used ESP or RESP (restrained ESP) charge models.

Probing Local Electrostatics of Glycine in Aqueous Solution by THz Spectroscopy

Based upon precise terahertz (THz) measurements of the solvated amino acid glycine and accompanying ab-initio molecular-dynamics simulations, we show that the N-C-C-O open/close mode at 315 cm-1 serves as a sensitive, label-free probe for the local protonation of the amide group. Experimentally, we can show that this holds not only for glycine but also for diglycine and valine. The approach is more general, since the changes due to protonation result in intensity changes which can be probed by THz time domain (0-50 cm-1 ) as well as by precise THz-FT spectroscopy (50-400 cm-1 ). A detailed analysis allows us to directly correlate the titration spectra with pKa values. This demonstrates the potential of THz spectroscopy to probe the charge state of a natural amino acid in water in a label-free manner.

Catalytic Principles from Natural Enzymes and Translational Design Strategies for Synthetic Catalysts

As biocatalysts, enzymes are characterized by their high catalytic efficiency and strong specificity but are relatively fragile by requiring narrow and specific reactive conditions for activity. Synthetic catalysts offer an opportunity for more chemical versatility operating over a wider range of conditions but currently do not reach the remarkable performance of natural enzymes. Here we consider some new design strategies based on the contributions of nonlocal electric fields and thermodynamic fluctuations to both improve the catalytic step and turnover for rate acceleration in arbitrary synthetic catalysts through bioinspired studies of natural enzymes. With a focus on the enzyme as a whole catalytic construct, we illustrate the translational impact of natural enzyme principles to synthetic enzymes, supramolecular capsules, and electrocatalytic surfaces.

Supramolecular kinetic effects by pillararenes: the synergism between spatiotemporal and preorganization concepts in decarboxylation reactions

Spatiotemporal and preorganization factors were both responsible for the catalytic and inhibitory supramolecular effects in decarboxylation reactions.