Reactions In Biological Systems Research Articles

QM/MM Free Energy Calculations of Long-Range Biological Protonation Dynamics by Adaptive and Focused Sampling.

Water-mediated proton transfer reactions are central for catalytic processes in a wide range of biochemical systems, ranging from biological energy conversion to chemical transformations in the metabolism. Yet, the accurate computational treatment of such complex biochemical reactions is highly challenging and requires the application of multiscale methods, in particular hybrid quantum/classical (QM/MM) approaches combined with free energy simulations. Here, we combine the unique exploration power of new advanced sampling methods with density functional theory (DFT)-based QM/MM free energy methods for multiscale simulations of long-range protonation dynamics in biological systems. In this regard, we show that combining multiple walkers/well-tempered metadynamics with an extended system adaptive biasing force method (MWE) provides a powerful approach for exploration of water-mediated proton transfer reactions in complex biochemical systems. We compare and combine the MWE method also with QM/MM umbrella sampling and explore the sampling of the free energy landscape with both geometric (linear combination of proton transfer distances) and physical (center of excess charge) reaction coordinates and show how these affect the convergence of the potential of mean force (PMF) and the activation free energy. We find that the QM/MM-MWE method can efficiently explore both direct and water-mediated proton transfer pathways together with forward and reverse hole transfer mechanisms in the highly complex proton channel of respiratory Complex I, while the QM/MM-US approach shows a systematic convergence of selected long-range proton transfer pathways. In this regard, we show that the PMF along multiple proton transfer pathways is recovered by combining the strengths of both approaches in a QM/MM-MWE/focused US (FUS) scheme and reveals new mechanistic insight into the proton transfer principles of Complex I. Our findings provide a promising basis for the quantitative multiscale simulations of long-range proton transfer reactions in biological systems.

Deciphering the Roles of Interfacial Amino Acids in Inter-Protein Charge Transport.

Elucidating charge transport (CT) through proteins is critical for gaining insights into ubiquitous CT chain reactions in biological systems and developing high-performance bioelectronic devices. While intra-protein CT has been extensively studied, crucial knowledge about inter-protein CT via interfacial amino acids is still absent due to the structural complexity. Herein, by loading cytochrome c (Cyt c) on well-defined peptide self-assembled monolayers to mimic the protein-protein interface, we provide a precisely controlled platform for identifying the roles of interfacial amino acids in solid-state CT via peptide-Cyt c junctions. The terminal amino acid of peptides serves as a fine-tuning factor for both the interfacial interaction between peptides and Cyt c and the immobilized Cyt c orientation, resulting in a nearly 10-fold difference in current through peptide-Cyt c junctions with varied asymmetry. This work provides a valuable platform for studying CT across proteins and contributes to the understanding of fundamental principles governing inter-protein CT.

Modeling and Analyzing Reaction Systems in Maude

Reaction Systems (RSs) are a successful computational framework for modeling systems inspired by biochemistry. An RS defines a set of rules (reactions) over a finite set of entities (e.g., molecules, proteins, genes, etc.). A computation in this system is performed by rewriting a finite set of entities (a computation state) using all the enabled reactions in the RS, thereby producing a new set of entities (a new computation state). The number of entities in the reactions and in the computation states can be large, making the analysis of RS behavior difficult without a proper automated support. In this paper, we use the Maude language—a programming language based on rewriting logic—to define a formal executable semantics for RSs, which can be used to precisely simulate the system behavior as well as to perform reachability analysis over the system computation space. Then, by enriching the proposed semantics, we formalize a forward slicer algorithm for RSs that allows us to observe the evolution of the system on both the initial input and a fragment of it (the slicing criterion), thus facilitating the detection of forward causality and influence relations due to the absence/presence of some entities in the slicing criterion. The pursued approach is illustrated by a biological reaction system that models a gene regulation network for controlling the process of differentiation of T helper lymphocytes.

Uncertainty quantified discovery of chemical reaction systems via Bayesian scientific machine learning

The recently proposed Chemical Reaction Neural Network (CRNN) discovers chemical reaction pathways from time resolved species concentration data in a deterministic manner. Since the weights and biases of a CRNN are physically interpretable, the CRNN acts as a digital twin of a classical chemical reaction network. In this study, we employ a Bayesian inference analysis coupled with neural ordinary differential equations (ODEs) on this digital twin to discover chemical reaction pathways in a probabilistic manner. This allows for estimation of the uncertainty surrounding the learned reaction network. To achieve this, we propose an algorithm which combines neural ODEs with a preconditioned stochastic gradient langevin descent (pSGLD) Bayesian framework, and ultimately performs posterior sampling on the neural network weights. We demonstrate the successful implementation of this algorithm on several reaction systems by not only recovering the chemical reaction pathways but also estimating the uncertainty in our predictions. We compare the results of the pSGLD with that of the standard SGLD and show that this optimizer more efficiently and accurately estimates the posterior of the reaction network parameters. Additionally, we demonstrate how the embedding of scientific knowledge improves extrapolation accuracy by comparing results to purely data-driven machine learning methods. Together, this provides a new framework for robust, autonomous Bayesian inference on unknown or complex chemical and biological reaction systems.

Fenton Reaction in vivo and in vitro. Possibilities and Limitations.

The review considers the problem of hydrogen peroxide decomposition and hydroxyl radical formation in the presence of iron in vivo and in vitro. Analysis of the literature data allows us to conclude that, under physiological conditions, transport of iron, carried out with the help of carrier proteins, minimizes the possibility of appearance of free iron ions in cytoplasm of the cell. Under pathological conditions, when the process of transferring an iron ion from a donor protein to an acceptor protein can be disrupted due to modifications of the carrier proteins, iron ions can enter cytosol. However, at pH values close to neutral, which is typical for cytosol, iron ions are converted into water-insoluble hydroxides. This makes it impossible to decompose hydrogen peroxide according to the mechanism of the classical Fenton reaction. A similar situation is observed in vitro, since buffers with pH close to neutral are used to simulate free radical oxidation. At the same time, iron hydroxides are able to catalyze decomposition of hydrogen peroxide with formation of a hydroxyl radical. Decomposition of hydrogen peroxide with iron hydroxides is called Fenton-like reaction. Studying the features of Fenton-like reaction in biological systems is the subject of future research.

Various Carbonic Anhydrases in Physiopathological Events, Carbonic Anhydrase Inhibitors, and Hybrid Compounds

Abstract: Enzymes are highly specific catalysts that accelerate reactions in biological systems. Carbonic anhydrase (CA) is an enzyme found in plants, microorganisms, and vertebrates. CA catalyses CO2 hydration/ dehydration. There are different families and isoenzymes of CAs. Fifteen α-CA isoenzymes have been reported in humans. The status of CO2 hydration and dehydration is important for a variety of biological processes. CAs play an important role in many physiological and pathological events in several tissue types. Their levels are increased in some diseases; therefore, CA inhibition has been applied as a therapeutic option. However, the high diversity of these isoenzymes is an important consideration. Isoenzyme- specific CA inhibitors can reduce the side effects of treatment. Some agents containing additional sulfonamides approved for other therapeutic applications, such as topiramate, celecoxib/valdecoxib, sulpiride, and famotidine, have inhibitory effects on CA isoenzymes. These bind to the zinc ion in the CA active site. Recently, research has been conducted on the use of a hybrid form of active ingredient and a CA inhibitor. CA inhibitor-NSAID hybrid compounds demonstrated more efficacy than NSAIDs in arthritis, which has attracted further attention of researchers in conducting research on CA-hybrid drugs.

Artificial Small Molecules as Cofactors and Biomacromolecular Building Blocks in Synthetic Biology: Design, Synthesis, Applications, and Challenges.

Enzymes are essential catalysts for various chemical reactions in biological systems and often rely on metal ions or cofactors to stabilize their structure or perform functions. Improving enzyme performance has always been an important direction of protein engineering. In recent years, various artificial small molecules have been successfully used in enzyme engineering. The types of enzymatic reactions and metabolic pathways in cells can be expanded by the incorporation of these artificial small molecules either as cofactors or as building blocks of proteins and nucleic acids, which greatly promotes the development and application of biotechnology. In this review, we summarized research on artificial small molecules including biological metal cluster mimics, coenzyme analogs (mNADs), designer cofactors, non-natural nucleotides (XNAs), and non-natural amino acids (nnAAs), focusing on their design, synthesis, and applications as well as the current challenges in synthetic biology.

High-Performance Recognition, Cell-Imaging, and Efficient Removal of Carbon Monoxide toward a Palladium-Mediated Fluorescent Sensing Platform.

Novel high-performance fluorescent approaches have always significant demand for room-temperature detection of carbon monoxide (CO), which is highly toxic even at low concentration levels and is not easy to recognize due to its colorless and odorless nature. In this paper, we constructed a palladium-mediated fluorescence turn-on sensing platform (TPANN-Pd) for the recognition of CO at room temperature, revealing simultaneously quick response speed (<30 s), excellent selectivity, superior sensitivity, and low detection limit (∼160 nM for CORM-3, ∼1.7 ppb for CO vapor). Moreover, rapid detection and efficient removal (24%) from the air by naked-eye vision has been successfully realized based on TPANN-Pd supramolecular gels. Furthermore, the developed sensing platform was elucidated with low cytotoxicity and high cellular uptake, and it was successfully applied to CO imaging in living cells, providing real-time monitoring of potential CO-involved reactions in biological systems.

Enzymatic reactions towards aldehydes: An overview.

Many aldehydes are volatile compounds with distinct and characteristic olfactory properties. The aldehydic functional group is reactive and, as such, an invaluable chemical multi-tool to make all sorts of products. Owing to the reactivity, the selective synthesis of aldehydic is a challenging task. Nature has evolved a number of enzymatic reactions to produce aldehydes, and this review provides an overview of aldehyde-forming reactions in biological systems and beyond. Whereas some of these biotransformations are still in their infancy in terms of synthetic applicability, others are developed to an extent that allows their implementation as industrial biocatalysts.

Biomanufacturing by In Vitro Biotransformation (ivBT) Using Purified Cascade Multi-enzymes.

In vitro biotransformation (ivBT) refers to the use of an artificial biological reaction system that employs purified enzymes for the one-pot conversion of low-cost materials into biocommodities such as ethanol, organic acids, and amino acids. Unshackled from cell growth and metabolism, ivBT exhibits distinct advantages compared with metabolic engineering, including but not limited to high engineering flexibility, ease of operation, fast reaction rate, high product yields, and good scalability. These characteristics position ivBT as a promising next-generation biomanufacturing platform. Nevertheless, challenges persist in the enhancement of bulk enzyme preparation methods, the acquisition of enzymes with superior catalytic properties, and the development of sophisticated approaches for pathway design and system optimization. In alignment with the workflow of ivBT development, this chapter presents a systematic introduction to pathway design, enzyme mining and engineering, system construction, and system optimization. The chapter also proffers perspectives on ivBT development.

Light-initiated 1,3-dipolar cycloaddition between dehydroalanines and tetrazoles: application to late-stage peptide and protein modifications.

As an easily introduced noncoded amino acid with unique electrophilicity distinct from the 20 natural amino acids, dehydroalanine (Dha) is not only a precise protein post-translational modification (PTM) insertion tool, but also a promising multifunctional labelling site for peptides and proteins. However, achieving a balance between the reaction rate and mild reaction conditions has been a major challenge in developing novel Dha-modified strategies. Rapid, efficient, and mild Dha modification strategies are highly desired. Additionally, catalyst-free photocontrollable reactions for Dha-containing peptide and protein modification have yet to be developed. Here, we report a photoinitiated 1,3-dipolar cycloaddition reaction between Dha and 2,5-diaryl tetrazoles. Under low-power UV lamp irradiation, this reaction is completed within minutes without catalysis, resulting in a fluorescent pyrazoline-modified peptide or protein with excellent chemoselectivity for Dha residues. Notably, this reaction exhibits complete site-specificity in the modification of thiostrepton, a natural antimicrobial peptide containing multiple Dha residues (Dha3, Dha16, and Dha17), within 20 minutes in high yields. This is currently the fastest reaction for modifying the Dha residue in thiostrepton with clear site-specificity towards Dha16. This photoinitiated reaction also provides a chemoselective strategy for precise functionalization of proteins. Additionally, the rapidity and efficiency of the reaction minimize UV light damage to the biological reaction system. Combined with fluorogenic properties, this photo-controllable methodology can be applied to live cell imaging, further broadening the application scope of the Dha modification methodology.

A colorimetric and fluorometric molecular system for discriminative detection of palladium acetate and CO cell imaging

A novel fluorophore (NAP-PMA) has been constructed through appending 2-pyridinemethanamine to naphthalimide. The air and moisture stable fluorophore were adopted as a colorimetric and fluorometric probe for palladium cation, revealing simultaneously good selectivity, high sensitivity and low detection limit (22.5 nM). Moreover, NAP-PMA not only exhibited a visible naked-eye color change from yellowish green to pink, but also displayed highly selective recognition to palladium acetate. In addition, NAP-PMA could be used as paper strips to quantitatively detect Pd2+ in water. Surprisingly, the developed sensing platform NAP-PMA-Pd is capable of detecting CO in living cells by “turn on” mode with high selectivity and stability, providing a potential real-time monitor for CO-involved reactions in biological systems.

Bottom-up Design of Organic Selenide Interfaces for Sensitive Electrocatalytic Detection of Peroxynitrite: A Fundamental Investigation and Application

Peroxynitrite (PON) is a potent oxidative stress species that has been linked with both oxidation and nitration reactions in biological systems. It emerged as a major cytotoxic agent that is implicated in a host of pathophysiological conditions. Reports emphasized the deleterious physiological reactivity of peroxynitrite with different cellular targets including DNA, proteins, and lipids in cell membranes. This oxidant has also been linked to cytoprotective roles under certain conditions. The balance between the deleterious reactivity and its potential cytoprotective roles of peroxynitrite depends on the dynamic concentration of this species. However, accurate determination of peroxynitrite concentration is inherently difficult particularly in biological systems. Various methods for peroxynitrite determination have been reported including indirect spectroscopic assays and, recently, direct electrochemical methods. While the development of electrochemical sensors for PON is currently a very active field, viable electrochemical probes for PON detection and quantification are still relatively illusive.In this work, we prepared and characterized a series of functional thin film materials based on organic diphenyl selenides on graphite electrodes and used these interfaces to compare and contrast their performance in terms of electrochemical determination of peroxynitrite.We will describe the preparation and grafting of the catalytic material based on the electrodeposition of various organic aminodiphenyl selenides on graphite electrodes. Several physicochemical methods including Scanning Electron Microscopy (SEM), Energy Dispersive X-ray spectroscopy (EDX) and X-ray Photoelectron Spectroscopy (XPS) were used to characterize the resulting modified interfaces. We will describe the performance of resulting selenide thin films as peroxynitrite sensing interfaces using voltammetry and amperometry. The grafted thin film materials show a significant enhancement in peroxynitrite oxidative current compared to controls under the same conditions. For all selenides tested, we show that the enhancement in peroxynitrite signal is the result of an electrocatalytic mechanism where the grafted aniline selenide-based material at the oxidized state mediates the electrocatalytic oxidation of peroxynitrite. We will compare and contrast the performance of the various selenide systems and explore if the modulation of the electronic properties of the selenium catalytic center results in proportional changes in PON catalytic efficiency. Figure 1

Multifunctional nanosystems sequentially regulating intratumor Fenton chemistry by remodeling the tumor microenvironment to reinforce chemodynamic therapy.

The particularity of the tumor microenvironment (TME) significantly limits the efficiency of chemodynamic therapy (CDT). Although various measures have been taken to improve the efficiency of CDT, how to organically integrate them into one nanosystem to achieve efficient synergy for CDT according to predetermined procedures is still an urgent problem to be solved. This work reported a multifunctional nanosystem, TPI@PPCAI, which comprised the inner triphenylphosphine modified D-α-Tocopheryl polyethylene glycol 1000 succinate (TPGS-PPh3) micelles loading iron-oxide nanoparticles (IONs), and the outer poly (dopamine-co-protocatechuic acid) (PDA-PA, PP) coating modified with carbonic anhydrase IX inhibitor (CAI). TPI@PPCAI remodeled TME by sequential function adjustment to make it suitable for the efficient Fenton reactions: CAI first inhibited the overexpressed CA IX to result in intracellular acidification, which combined with near-infrared light (NIR) irradiation to accelerate the PP coating degradation, thereby promoting the exposure and disintegration of the inner micellar structure to release TPGS-PPh3 and IONs. The TPGS-PPh3 further elevated the intracellular ROS basal level by targeting and interfering with the mitochondrial function. Therefore, the TME was transformed into an acidic microenvironment with high ROS levels, which vigorously promoted the Fenton reaction mediated by IONs with the aid of photothermal effect induced by PP coating via NIR irradiation, ultimately earning high-efficiency CDT on xenograft MDA-MB-231 tumor-bearing mice. This study improved the efficiency of Fenton reaction in biological systems through the practical design of nanostructures and provided a novel thought for ROS-mediated therapy.

Water acting as a catalytic promoter for electron-proton transfer in the Pt single atom catalyzed environmental reduction reactions

Water, which is the host of life, introduces many unusual features into the kinetics and energetics of biological reaction systems catalyzed by enzymes. Single atom catalyst has great potential to mimic biological enzymes in regard to special catalytic sites and high efficiency. Here we report a significant promotion by H2O in the environmental reduction of nitrobenzene on an environmentally friendly humic acid supported Pt single atom catalyst. No nitrobenzene conversion took place when only organic solvents were used while high activity of the catalyst was observed in aqueous mixtures (turnover frequency is as high as 1883 h−1). Experiments and density functional theory calculation show that H2O greatly decreased the energy barrier by enabling a biomimetic electron-proton transfer for the hydrogenation process even on single atom Pt catalyst, and a new reaction pathway with phenyl-λ1-azane as intermediate in the direct hydrogenation of nitrobenzene is proposed.

Kinetic investigations of the formation of iron(IV) oxido complexes

Oxido iron(IV) complexes are key intermediates in oxygenation reactions in biological systems. They can form during oxidation experiments with various oxidants such as oxygen, hydrogen peroxide, organoiodine compounds, or ozone. However, kinetic studies for these reactions are rare because the intermediates are usually labile. Here the results of a detailed investigation on the oxidation of iron(II) complexes with macrocyclic (e.g. TMC = tetramethylcyclam = 1,4,8,11-tetramethyl-1,4,8,11-tetraaza-cyclotetradecane) ligands are reported that provide a better understanding of the mechanisms of these reactions. For formation of the quite stable oxido iron complex with an amide derivative of TMC, activation parameters with ΔH ‡ = 28 ± 4 kJ·mol−1 and ΔS ‡ = −144 ± 15 J·mol−1·K−1 could be obtained that allowed postulation of an associative mechanism.

A Review on Versatile Eco-Friendly Applications of Microbial Proteases in Biomedical and Industrial Applications

Enzymes are the keystone for metabolism or the chemical reactions in biological systems. They help to build certain substances and break others down. Enzymes play a critical role in our bodies, industries and corporate sectors. Protease is an enzyme that helps break the peptide bonds present in the protein and separates the amino acids. Microbial proteases are the ones where the bacteria can produce the protease enzyme. Among many industrial enzymes, microbial protease has a versatile role in many fields like laundry, leather preparation, feather degradation, detergent preparation, biocontrol agents, optical lens cleaners, tannery, deproteinization of prawn shell, prevention of putrefaction of cutting oil, food preservatives, chelating agents, fodder additives, removal and degradation of polymeric substances (EPS), removal of hairs in buffalo hide, waste treatment, bioremediation process, reduction of waste-activated sludge and biofilm formation, degumming of silk, cosmetics (to remove glabellar-frown lines), cheese making, Meat tenderization, rehydration of goat skins and reduced water quantity, fibrin degradation, photographic, silver recovery from X-ray films, dairy industry, control harmful nematodes, fruit juice, and bakery, soybean paste, and sauce industry, pulp mills, alcohol production, fish processing wastes, prion degradation. Microbial protease is popularly used in the detergent industry, leather industry, textile industry, food industry, dairy industry, meat processing industry, bakery industry, pharmaceutical industry, etc.

The covalent reactivity of functionalized 5-hydroxy-butyrolactams is the basis for targeting of fatty acid binding protein 5 (FABP5) by the neurotrophic agent MT-21.

Covalently acting compounds experience a strong interest within chemical biology both as molecular probes in studies of fundamental biological mechanisms and/or as novel drug candidates. In this context, the identification of new classes of reactive groups is particularly important as these can expose novel reactivity modes and, consequently, expand the ligandable proteome. Here, we investigated the electrophilic reactivity of the 3-acyl-5-hydroxy-1,5-dihydro-2H-pyrrole-2-one (AHPO) scaffold, a heterocyclic motif that is e.g. present in various bioactive natural products. Our investigations were focused on the compound MT-21 - a simplified structural analogue of the natural product epolactaene - which is known to have both neurotrophic activity and ability to trigger apoptotic cell death. We found that the central N-acyl hemiaminal group of MT-21 can function as an electrophilic centre enabling divergent reactivity with both amine- and thiol-based nucleophiles, which furthermore translated to reactivity with proteins in both cell lysates and live cells. We found that in live cells MT-21 strongly engaged the lipid transport protein fatty acid-binding protein 5 (FABP5) by direct binding to a cysteine residue in the bottom of the ligand binding pocket. Through preparation of a series of MT-21 derivatives, we probed the specificity of this interaction which was found to be strongly dependent on subtle structural changes. Our study suggests that MT-21 may be employed as a tool compound in future studies of the biology of FABP5, which remains incompletely understood. Furthermore, our study has also made clear that other natural products containing the AHPO-motif may likewise possess covalent reactivity and that this property may underlie their biological activity.

Development of a PFAS reaction library: identifying plausible transformation pathways in environmental and biological systems.

Perfluoroalkyl and polyfluoroalkyl substances (PFAS) are used in many consumer applications due to their stain repellency, surfactant properties, ability to form water-proof coatings and use in fire suppression. The production, application, transport, use and disposal of PFAS and PFAS-treated products have resulted in their wide-spread occurrence in environmental and biological systems. Concern over exposure to PFAS and their transformation products and metabolites has necessitated the development of tools to predict the transformation of PFAS in environmental systems and metabolism in biological systems. We have developed reaction libraries for predicting transformation products and metabolites in a variety of environmental and biological reaction systems. These reaction libraries are based on generalized reaction schemes that encode the process science of PFAS reported in the peer-reviewed literature. The PFAS reaction libraries will be executed through the Chemical Transformation Simulator, a web-based tool that is available to the public. These reaction libraries are intended for predicting the environmental transformation and metabolism of PFAS only.

Regulation and Functional Complexity of the Chlorophyll-Binding Protein IsiA.

As the oldest known lineage of oxygen-releasing photosynthetic organisms, cyanobacteria play the key roles in helping shaping the ecology of Earth. Iron is an ideal transition metal for redox reactions in biological systems. Cyanobacteria frequently encounter iron deficiency due to the environmental oxidation of ferrous ions to ferric ions, which are highly insoluble at physiological pH. A series of responses, including architectural changes to the photosynthetic membranes, allow cyanobacteria to withstand this condition and maintain photosynthesis. Iron-stress-induced protein A (IsiA) is homologous to the cyanobacterial chlorophyll (Chl)-binding protein, photosystem II core antenna protein CP43. IsiA is the major Chl-containing protein in iron-starved cyanobacteria, binding up to 50% of the Chl in these cells, and this Chl can be released from IsiA for the reconstruction of photosystems during the recovery from iron limitation. The pigment–protein complex (CPVI-4) encoded by isiA was identified and found to be expressed under iron-deficient conditions nearly 30years ago. However, its precise function is unknown, partially due to its complex regulation; isiA expression is induced by various types of stresses and abnormal physiological states besides iron deficiency. Furthermore, IsiA forms a range of complexes that perform different functions. In this article, we describe progress in understanding the regulation and functions of IsiA based on laboratory research using model cyanobacteria.