Do Ionic Liquids Exhibit the Required Characteristics to Dissolve, Extract, Stabilize, and Purify Proteins? Past-Present-Future Assessment.

Proteins are highly labile molecules, thus requiring the presence of appropriate solvents and excipients in their liquid milieu to keep their stability and biological activity. In this field, ionic liquids (ILs) have gained momentum in the past years, with a relevant number of works reporting their successful use to dissolve, stabilize, extract, and purify proteins. Different approaches in protein-IL systems have been reported, namely, proteins dissolved in (i) neat ILs, (ii) ILs as co-solvents, (iii) ILs as adjuvants, (iv) ILs as surfactants, (v) ILs as phase-forming components of aqueous biphasic systems, and (vi) IL-polymer-protein/peptide conjugates. Herein, we critically analyze the works published to date and provide a comprehensive understanding of the IL-protein interactions affecting the stability, conformational alteration, unfolding, misfolding, and refolding of proteins while providing directions for future studies in view of imminent applications. Overall, it has been found that the stability or purification of proteins by ILs is bispecific and depends on the structure of both the IL and the protein. The most promising IL-protein systems are identified, which is valuable when foreseeing market applications of ILs, e.g., in "protein packaging" and "detergent applications". Future directions and other possibilities of IL-protein systems in light-harvesting and biotechnology/biomedical applications are discussed.

Non-Native Site-Selective Enzyme Catalysis.

The ability to site-selectively modify equivalent functional groups in a molecule has the potential to streamline syntheses and increase product yields by lowering step counts. Enzymes catalyze site-selective transformations throughout primary and secondary metabolism, but leveraging this capability for non-native substrates and reactions requires a detailed understanding of the potential and limitations of enzyme catalysis and how these bounds can be extended by protein engineering. In this review, we discuss representative examples of site-selective enzyme catalysis involving functional group manipulation and C-H bond functionalization. We include illustrative examples of native catalysis, but our focus is on cases involving non-native substrates and reactions often using engineered enzymes. We then discuss the use of these enzymes for chemoenzymatic transformations and target-oriented synthesis and conclude with a survey of tools and techniques that could expand the scope of non-native site-selective enzyme catalysis.

Soluble TREM2 inhibits secondary nucleation of Aß fibrillization and enhances cellular uptake of fibrillar Aß.

Triggering receptor expressed on myeloid cells 2 (TREM2) is a single-pass transmembrane receptor of the immunoglobulin superfamily that is secreted in a soluble (sTREM2) form. Mutations in TREM2 have been linked to increased risk of Alzheimer's disease (AD). A prominent neuropathological component of AD is deposition of the amyloid-ß (Aß) into plaques, particularly Aß40 and Aß42. While the membrane-bound form of TREM2 is known to facilitate uptake of Aß fibrils and the polarization of microglial processes toward amyloid plaques, the role of its soluble ectodomain, particularly in interactions with monomeric or fibrillar Aß, has been less clear. Our results demonstrate that sTREM2 does not bind to monomeric Aß40 and Aß42, even at a high micromolar concentration, while it does bind to fibrillar Aß42 and Aß40 with equal affinities (2.6 ± 0.3 µM and 2.3 ± 0.4 µM). Kinetic analysis shows that sTREM2 inhibits the secondary nucleation step in the fibrillization of Aß, while having little effect on the primary nucleation pathway. Furthermore, binding of sTREM2 to fibrils markedly enhanced uptake of fibrils into human microglial and neuroglioma derived cell lines. The disease-associated sTREM2 mutant, R47H, displayed little to no effect on fibril nucleation and binding, but it decreased uptake and functional responses markedly. We also probed the structure of the WT sTREM2-Aß fibril complex using integrative molecular modeling based primarily on the cross-linking mass spectrometry data. The model shows that sTREM2 binds fibrils along one face of the structure, leaving a second, mutation-sensitive site free to mediate cellular binding and uptake.

Noise-independent route toward the genesis of a COMPACT ansatz for molecular energetics: A dynamic approach.

Recent advances in quantum information and quantum science have inspired the development of various compact, dynamically structured ansätze that are expected to be realizable in Noisy Intermediate-Scale Quantum (NISQ) devices. However, such ansätze construction strategies hitherto developed involve considerable measurements, and thus, they deviate significantly in the NISQ platform from their ideal structures. Therefore, it is imperative that the usage of quantum resources be minimized while retaining the expressivity and dynamical structure of the ansatz that can adapt itself depending on the degree of correlation. We propose a novel ansatz construction strategy based on the ab initio many-body perturbation theory that requires no pre-circuit measurement and, thus, remains structurally unaffected by any hardware noise. The accuracy and quantum complexity associated with the ansatz are solely dictated by a pre-defined perturbative order, as desired, and, hence, are tunable. Furthermore, the underlying perturbative structure of the ansatz construction pipeline enables us to decompose any high-rank excitation that appears in higher perturbative orders into the product of various low-rank operators, and it thus keeps the execution gate-depth to its minimum. With a number of challenging applications on strongly correlated systems, we demonstrate that our ansatz performs significantly better, both in terms of accuracy, parameter count, and circuit depth, in comparison to the allied unitary coupled cluster based ansätze.

Toward a resource-optimized dynamic quantum algorithm via non-iterative auxiliary subspace corrections.

Recent quantum algorithms pertaining to electronic structure theory primarily focus on the threshold-based dynamic construction of ansatz by selectively including important many-body operators. These methods can be made systematically more accurate by tuning the threshold to include a greater number of operators into the ansatz. However, such improvements come at the cost of rapid proliferation of the circuit depth, especially for highly correlated molecular systems. In this work, we address this issue by the development of a novel theoretical framework that relies on the segregation of an ansatz into a dynamically selected core "principal" component, which is, by construction, adiabatically decoupled from the remaining operators. This enables us to perform computations involving the principal component using extremely shallow-depth circuits, whereas the effect of the remaining "auxiliary" component is folded into the energy function via a cost-efficient non-iterative correction, ensuring the requisite accuracy. We propose a formalism that analytically predicts the auxiliary parameters from the principal ones, followed by a suite of non-iterative auxiliary subspace correction techniques with different levels of sophistication. The auxiliary subspace corrections incur no additional quantum resources yet complement an inadequately expressive core of the ansatz to recover a significant amount of electronic correlations. We have numerically validated the resource efficiency and accuracy of our formalism with a number of strongly correlated molecular systems.

A Synergistic Approach towards Optimization of Coupled Cluster Amplitudes by Exploiting Dynamical Hierarchy.

The coupled cluster iteration scheme for determining the cluster amplitudes involves a set of nonlinearly coupled difference equations. In the space spanned by the amplitudes, the set of equations are analyzed as a multivariate time-discrete map where the concept of time appears in an implicit manner. With the observation that the cluster amplitudes have difference in their relaxation timescales with respect to the distributions of their magnitudes, the coupled cluster iteration dynamics are considered as a synergistic motion of coexisting slow and fast relaxing modes, manifesting a dynamical hierarchical structure. With the identification of the highly damped auxiliary amplitudes, their time variation can be neglected compared to the principal amplitudes which take much longer time to reach the fixed points. We analytically establish the adiabatic approximation where each of these auxiliary amplitudes are expressed as unique parametric functions of the collective principal amplitudes, allowing us to study the optimization with the latter taken as the independent degrees of freedom. Such decoupling of the amplitudes significantly reduces the computational scaling without sacrificing the accuracy in the ground state energy as demonstrated by a number of challenging molecular applications. A road-map to treat higher order post-adiabatic effects is also discussed.

Development of a compact Ansatz via operator commutativity screening: Digital quantum simulation of molecular systems.

Recent advancements in quantum information and quantum technology have stimulated a good deal of interest in the development of quantum algorithms toward the determination of the energetics and properties of many-fermionic systems. While the variational quantum eigensolver is the most optimal algorithm in the noisy intermediate scale quantum era, it is imperative to develop compact Ansätze with low-depth quantum circuits that are physically realizable in quantum devices. Within the unitary coupled cluster framework, we develop a disentangled Ansatz construction protocol that can dynamically tailor an optimal Ansatz using the one- and two-body cluster operators and a selection of rank-two scatterers. The construction of the Ansatz may potentially be performed in parallel over multiple quantum processors through energy sorting and operator commutativity prescreening. With a significant reduction in the circuit depth toward the simulation of molecular strong correlation, our dynamic Ansatz construction protocol is shown to be highly accurate and resilient to the noisy circumstances of the near-term quantum hardware.

Machine learning aided dimensionality reduction toward a resource efficient projective quantum eigensolver: Formal development and pilot applications.

In recent times, a variety of hybrid quantum-classical algorithms have been developed that aim to calculate the ground state energies of molecular systems on Noisy Intermediate-Scale Quantum (NISQ) devices. Albeit the utilization of shallow depth circuits in these algorithms, the optimization of ansatz parameters necessitates a substantial number of quantum measurements, leading to prolonged runtimes on the scantly available quantum hardware. Through our work, we lay the general foundation for an interdisciplinary approach that can be used to drastically reduce the dependency of these algorithms on quantum infrastructure. We showcase these pertinent concepts within the framework of the recently developed Projective Quantum Eigensolver (PQE) that involves iterative optimization of the nonlinearly coupled parameters through repeated residue measurements on quantum hardware. We demonstrate that one may perceive such a nonlinear optimization problem as a collective dynamic interplay of fast and slow relaxing modes. As such, the synergy among the parameters is exploited using an on-the-fly supervised machine learning protocol that dynamically casts the PQE optimization into a smaller subspace by reducing the effective degrees of freedom. We demonstrate analytically and numerically that our proposed methodology ensures a drastic reduction in the number of quantum measurements necessary for the parameter updates without compromising the characteristic accuracy. Furthermore, the machine learning model may be tuned to capture the noisy data of NISQ devices, and thus the predicted energy is shown to be resilient under a given noise model.

Exploring the activation pathway and Gi-coupling specificity of the µ-opioid receptor.

Understanding the activation mechanism of the µ-opioid receptor (µ-OR) and its selective coupling to the inhibitory G protein (Gi) is vital for pharmaceutical research aimed at finding treatments for the opioid overdose crisis. Many attempts have been made to understand the mechanism of the µ-OR activation, following the elucidation of new crystal structures such as the antagonist- and agonist-bound µ-OR. However, the focus has not been placed on the underlying energetics and specificity of the activation process. An energy-based picture would not only help to explain this coupling but also help to explore why other possible options are not common. For example, one would like to understand why µ-OR is more selective to Gi than a stimulatory G protein (Gs). Our study used homology modeling and a coarse-grained model to generate all of the possible "end states" of the thermodynamic cycle of the activation of µ-OR. The end points were further used to generate reasonable intermediate structures of the receptor and the Gi to calculate two-dimensional free energy landscapes. The results of the landscape calculations helped to propose a plausible sequence of conformational changes in the µ-OR and Gi system and for exploring the path that leads to its activation. Furthermore, in silico alanine scanning calculations of the last 21 residues of the C terminals of Gi and Gs were performed to shed light on the selective binding of Gi to µ-OR. Overall, the present work appears to demonstrate the potential of multiscale modeling in exploring the action of G protein-coupled receptors.

Directed Evolution of an Iron(II)- and α-Ketoglutarate-Dependent Dioxygenase for Site-Selective Azidation of Unactivated Aliphatic C-H Bonds.

FeII - and α-ketoglutarate-dependent halogenases and oxygenases can catalyze site-selective functionalization of C-H bonds via a variety of C-X bond forming reactions, but achieving high chemoselectivity for functionalization using non-native functional groups remains rare. The current study shows that directed evolution can be used to engineer variants of the dioxygenase SadX that address this challenge. Site-selective azidation of succinylated amino acids and a succinylated amine was achieved as a result of mutations throughout the SadX structure. The installed azide group was reduced to a primary amine, and the succinyl group required for azidation was enzymatically cleaved to provide the corresponding amine. These results provide a promising starting point for evolving additional SadX variants with activity on structurally distinct substrates and for enabling enzymatic C-H functionalization with other non-native functional groups.

Histidine protonation states are key in the LigI catalytic reaction mechanism.

Lignin is one of the world's most abundant organic polymers, and 2-pyrone-4,6-dicarboxylate lactonase (LigI) catalyzes the hydrolysis of 2-pyrone-4,6-dicarboxylate (PDC) in the degradation of lignin. The pH has profound effects on enzyme catalysis and therefore we studied this in the context of LigI. We found that changes of the pH mostly affects surface residues, while the residues at the active site are more subject to changes of the surrounding microenvironment. In accordance with this, a high pH facilitates the deprotonation of the substrate. Detailed free energy calculations by the empirical valence bond (EVB) approach revealed that the overall hydrolysis reaction is more likely when the three active site histidines (His31, His33 and His180) are protonated at the ɛ site, however, protonation at the δ site may be favored during specific steps of the reaction. Our studies have uncovered the determinant role of the protonation state of the active site residues His31, His33 and His180 in the hydrolysis of PDC.

Directed Evolution of Flavin-Dependent Halogenases for Site- and Atroposelective Halogenation of 3-Aryl-4(3H)-Quinazolinones via Kinetic or Dynamic Kinetic Resolution.

In this study, we engineer a variant of the flavin-dependent halogenase RebH that catalyzes site- and atroposelective halogenation of 3-aryl-4(3H)-quinazolinones via kinetic or dynamic kinetic resolution. The required directed evolution uses a combination of random and site-saturation mutagenesis, substrate walking using two probe substrates, and a two-tiered screening approach involving the analysis of variant conversion and then enantioselectivity of improved variants. The resulting variant, 3-T, provides >99:1 e.r. for the (M)-atropisomer of the major brominated product, 25-fold improved conversion, and 91-fold improved site selectivity relative to the parent enzyme on the probe substrate used in the final rounds of evolution. This high activity and selectivity translate well to several additional substrates with varied steric and electronic properties. Computational modeling and docking simulations are used to rationalize the effects of key mutations on substrate binding. Given the range of substrates that have been used for atroposelective synthesis via electrophilic halogenation in the literature, these results suggest that flavin-dependent halogenases (FDHs) could find many additional applications for atroposelective catalysis. More broadly, this study highlights how RebH can be engineered to accept structurally diverse substrates that enable its use for enantioselective catalysis.

The Single-Component Flavin Reductase/Flavin-Dependent Halogenase AetF is a Versatile Catalyst for Selective Bromination and Iodination of Arenes and Olefins.

Flavin-dependent halogenases (FDHs) natively catalyze selective halogenation of electron rich aromatic and enolate groups. Nearly all FDHs reported to date require a separate flavin reductase to supply them with FADH2 , which complicates biocatalysis applications. In this study, we establish that the single component flavin reductase/flavin dependent halogenase AetF catalyzes halogenation of a diverse set of substrates using a commercially available glucose dehydrogenase to drive its halogenase activity. High site selectivity, activity on relatively unactivated substrates, and high enantioselectivity for atroposelective bromination and bromolactonization was demonstrated. Site-selective iodination and enantioselective cycloiodoetherification was also possible using AetF. The substrate and reaction scope of AetF suggest that it has the potential to greatly improve the utility of biocatalytic halogenation.

Exploring the Activation Process of the ß2AR-Gs Complex.

G-Protein-coupled receptors (GPCRs) belong to an important family of integral membrane receptor proteins that are essential for a variety of transmembrane signaling process, such as vision, olfaction, and hormone responses. They are also involved in many human diseases (Alzheimer's, heart diseases, etc.) and are therefore common drug targets. Thus, understanding the details of the GPCR activation process is a task of major importance. Various types of crystal structures of GPCRs have been solved either at stable end-point states or at possible intermediate states. However, the detailed mechanism of the activation process is still poorly understood. For example, it is not completely clear when the nucleotide release from the G protein occurs and how the key residues on α5 contribute to the coupling process and further affect the binding specificity. In this work we show by free energy analysis that the guanosine diphosphate (GDP) molecule could be released from the Gs protein when the binding cavity is half open. This occurs during the transition to the Gs open state, which is the rate-determining step in the system conformational change. We also account for the experimentally observed slow-down effects by the change of the reaction barriers after mutations. Furthermore, we identify potential key residues on α5 and validated their significance by site-directed mutagenesis, which illustrates that computational works have predictive value even for complex biophysical systems. The methodology of the current work may be applied to other biophysical systems of interest.

EF-Tu and EF-G are activated by allosteric effects.

Many cellular processes are controlled by GTPases, and gaining quantitative understanding of the activation of such processes has been a major challenge. In particular, it is crucial to obtain reliable free-energy surfaces for the relevant reaction paths both in solution and in GTPases active sites. Here, we revisit the energetics of the activation of EF-G and EF-Tu by the ribosome and explore the nature of the catalysis of the GTPase reaction. The comparison of EF-Tu to EF-G allows us to explore the impact of possible problems with the available structure of EF-Tu. Additionally, mutational effects are used for a careful validation of the emerging conclusions. It is found that the reaction may proceed by both a two-water mechanism and a one-water (GTP as a base) mechanism. However, in both cases, the activation involves a structural allosteric effect, which is likely to be a general-activation mechanism for all GTPases.

Exploring the Mechanism of Covalent Inhibition: Simulating the Binding Free Energy of α-Ketoamide Inhibitors of the Main Protease of SARS-CoV-2.

The development of reliable ways of predicting the binding free energies of covalent inhibitors is a challenge for computer-aided drug design. Such development is important, for example, in the fight against the SARS-CoV-2 virus, in which covalent inhibitors can provide a promising tool for blocking Mpro, the main protease of the virus. This work develops a reliable and practical protocol for evaluating the binding free energy of covalent inhibitors. Our protocol presents a major advance over other approaches that do not consider the chemical contribution of the binding free energy. Our strategy combines the empirical valence bond method for evaluating the reaction energy profile and the PDLD/S-LRA/ß method for evaluating the noncovalent part of the binding process. This protocol has been used in the calculations of the binding free energy of an α-ketoamide inhibitor of Mpro. Encouragingly, our approach reproduces the observed binding free energy. Our study of covalent inhibitors of cysteine proteases indicates that in the choice of an effective warhead it is crucial to focus on the exothermicity of the point on the free energy surface of a peptide cleavage that connects the acylation and deacylation steps. Overall, we believe that our approach should provide a powerful and effective method for in silico design of covalent drugs.

Exploring alternative catalytic mechanisms of the Cas9 HNH domain.

Understanding the reaction mechanism of CRISPR-associated protein 9 (Cas9) is crucial for the application of programmable gene editing. Despite the availability of the structures of Cas9 in apo- and substrate-bound forms, the catalytically active structure is still unclear. Our first attempt to explore the catalytic mechanism of Cas9 HNH domain has been based on the reasonable assumption that we are dealing with the same mechanism as endonuclease VII, including the assumption that the catalytic water is in the first shell of the Mg2+ . Trying this mechanism with the cryo-EM structure forced us to induce significant structural change driven by the movement of K848 (or other positively charged residue) close to the active site to facilitate the proton transfer step. In the present study, we explore a second reaction mechanism where the catalytic water is in the second shell of the Mg2+ and assume that the cryo-EM structure by itself is a suitable representation of a catalytic-ready structure. The alternative mechanism indicates that if the active water is from the second shell, then the calculated reaction barrier is lower compared with the corresponding barrier when the water comes from the first shell.

Protein packaging in ionic liquid mixtures: an ecofriendly approach towards the improved stability of ß-lactoglobulin in cholinium-based mixed ionic liquids.

Ionic liquid (IL)-protein interaction studies are well documented; nonetheless, some families of ILs possess high toxicity which leads to the perturbation of biomolecules. However, ILs can be suitably designed by tweaking the constituent ions and also by amalgamating the mixture that stabilises the protein against the denaturing effect of another IL. To address this, the present study has explored the role of IL mixtures in imparting structural stability to protein ß-lactoglobulin (ß-LG). Previously, it was demonstrated that choline iodide ([Chn][I]) had an adverse effect on the native structure of ß-LG. In order to counteract the deleterious action of [Chn][I], four IL mixtures (choline acetate [Chn][Ac] + [Chn][I] (MCACI); choline bitartrate [Chn][Bit] + [Chn][I] (MCBCI); choline chloride [Chn][Cl] + [Chn][I] (MCCCI); and choline dihydrogenphosphate [Chn][Dhp] + [Chn][I] (MCDCI)) were prepared in different ratios and their effects on the structural stability of ß-LG were investigated. The UV-visible and fluorescence spectroscopy results revealed that ß-LG achieved conformational changes with the addition of aqueous solutions containing mixtures of these ILs as compared to [Chn][I] alone. In near UV-CD spectroscopy, we observed that these four mixtures of ILs preserved the structure of ß-LG by maintaining the tertiary structure. The dynamic light scattering (DLS) results demonstrated that the aqueous solutions containing IL mixtures decreased the dH values of ß-LG, eventually keeping the compact structure of ß-LG. These results confirm that the four biocompatible IL mixtures reduce the unavoidable aggregates of ß-LG in the presence of [Chn][I]. Additionally, from the thermal fluorescence analysis, it was observed that the thermal stability of ß-LG was enhanced by the four IL mixtures, thus counteracting the deleterious effect of [Chn][I] on ß-LG. To the best of our knowledge, this work for the first time has demonstrated the role of choline-based IL mixtures in the structural transition of ß-LG. The IL mixtures successfully enhanced the stability of the protein by reducing the perturbation caused by one of the components of the IL mixtures, thus amplifying the advantages of the other components. Overall, these results might find implications for understanding the role of IL mixtures towards protein folding/unfolding and pave a new direction for the development of eco-friendly protein-protective additives.

Ionic-Liquid-Mediated Extraction and Separation Processes for Bioactive Compounds: Past, Present, and Future Trends.

Ionic liquids (ILs) have been proposed as promising media for the extraction and separation of bioactive compounds from the most diverse origins. This critical review offers a compilation on the main results achieved by the use of ionic-liquid-based processes in the extraction and separation/purification of a large range of bioactive compounds (including small organic extractable compounds from biomass, lipids, and other hydrophobic compounds, proteins, amino acids, nucleic acids, and pharmaceuticals). ILs have been studied as solvents, cosolvents, cosurfactants, electrolytes, and adjuvants, as well as used in the creation of IL-supported materials for separation purposes. The IL-based processes hitherto reported, such as IL-based solid-liquid extractions, IL-based liquid-liquid extractions, IL-modified materials, and IL-based crystallization approaches, are here reviewed and compared in terms of extraction and separation performance. The key accomplishments and future challenges to the field are discussed, with particular emphasis on the major lacunas found within the IL community dedicated to separation processes and by suggesting some steps to overcome the current limitations.

Chemo-enzymatic synthesis of the exocyclic olefin isomer of thymidine monophosphate.

Exocyclic olefin variants of thymidylate (dTMP) recently have been proposed as reaction intermediates for the thymidyl biosynthesis enzymes found in many pathogenic organisms, yet synthetic reports on these materials are lacking. Here we report two strategies to prepare the exocyclic olefin isomer of dTMP, which is a putative reaction intermediate in pathogenic thymidylate biosynthesis and a novel nucleotide analog. Our most effective strategy involves preserving the existing glyosidic bond of thymidine and manipulating the base to generate the exocyclic methylene moiety. We also report a successful enzymatic deoxyribosylation of a non-aromatic nucleobase isomer of thymine, which provides an additional strategy to access nucleotide analogs with disrupted ring conjugation or with reduced heterocyclic bases. The strategies reported here are straightforward and extendable towards the synthesis of various pyrimidine nucleotide analogs, which could lead to compounds of value in studies of enzyme reaction mechanisms or serve as templates for rational drug design.