BIOPHYSICS. Comment on "Extreme electric fields power catalysis in the active site of ketosteroid isomerase"

Recent Advancements on Sustainable Electrochemical Water Splitting Hydrogen Energy Applications Based on Nanoscale Transition Metal Oxide (TMO) Substrates

The development of green hydrogen generation technologies is increasingly crucial to meeting the growing energy demand for sustainable and environmentally acceptable resources. Many obstacles in the advancement of electrodes prevented water electrolysis, long thought to be an eco-friendly method of producing hydrogen gas with no carbon emissions, from coming to fruition. Because of their great electrical conductivity, maximum supporting capacity, ease of modification in valence states, durability in hard environments, and high redox characteristics, transition metal oxides (TMOs) have recently captured a lot of interest as potential cathodes and anodes. Electrochemical water splitting is the subject of this investigation, namely the role of transition metal oxides as both active and supportive sites. It has suggested various approaches for the logical development of electrode materials based on TMOs. These include adjusting the electronic state, altering the surface structure to control its resistance to air and water, improving the flow of energy and matter, and ensuring the stability of the electrocatalyst in challenging conditions. In this comprehensive review, it has been covered the latest findings in electrocatalysis of the Oxygen Evolution Reaction (OER) and Hydrogen Evaluation Reaction (HER), as well as some of the specific difficulties, opportunities, and current research prospects in this field.

DFT study on CO 2 capture using boron, nitrogen, and phosphorus-doped C 20 in the presence of an electric field

Burning fossil fuels emits a significant amount of CO 2 , causing climate change concerns. CO 2 Capture and Storage (CCS) aims to reduce emissions, with fullerenes showing promise as CO 2 adsorbents. Recent research focuses on modifying fullerenes using an electric field. In light of this, we carried out DFT studies on some B, N, and P doped C 20 (C 20 - n X n , n = 0, 1, 2, and 3; X = B, N, and P) in the absence and presence of an electric field in the range of 0-0.02 a.u.. The cohesive energy was calculated to ensure their thermodynamic stability showing, that despite having lesser cohesive energies than C 20 , they appear in a favorable range. Moreover, the charge distribution for all structures was depicted using the ESP map. Most importantly, we evaluated the adsorption energy, height, and CO 2 angle, demonstrating the B and N-doped fullerenes had the stronger interaction with CO 2 , which by far exceeded C 20 's, improving its physisorption to physicochemical adsorption. Although the adsorption energy of P-doped fullerenes was not as satisfactory, in most cases, increasing the electric field led to enhancing CO 2 adsorption and incorporating chemical attributes to CO 2 -fullerene interaction. The HOMO-LUMO plots were obtained by which we discovered that unlike the P-doped C 20 , the surprising activity of B and N-doped C 20 s against CO 2 originates from a high concentration of the HOMO-LUMO orbitals on B, N and neighboring atoms. In the present article, we attempt to introduce more effective fullerene-based materials for CO 2 adsorption as well as strategies to enhance their efficiency and revealing adsorption nature over B, N, and P-doped fullerenes and in the end, hope to encourage more experimental research on these materials within growing electric field for CO 2 capture in the future.

Substitution Models of Protein Evolution with Selection on Enzymatic Activity

Substitution models of evolution are necessary for diverse evolutionary analyses including phylogenetic tree and ancestral sequence reconstructions. At the protein level, empirical substitution models are traditionally used due to their simplicity, but they ignore the variability of substitution patterns among protein sites. Next, in order to improve the realism of the modeling of protein evolution, a series of structurally constrained substitution models were presented, but still they usually ignore constraints on the protein activity. Here, we present a substitution model of protein evolution with selection on both protein structure and enzymatic activity, and that can be applied to phylogenetics. In particular, the model considers the binding affinity of the enzyme-substrate complex as well as structural constraints that include the flexibility of structural flaps, hydrogen bonds, amino acids backbone radius of gyration, and solvent-accessible surface area that are quantified through molecular dynamics simulations. We applied the model to the HIV-1 protease and evaluated it by phylogenetic likelihood in comparison with the best-fitting empirical substitution model and a structurally constrained substitution model that ignores the enzymatic activity. We found that accounting for selection on the protein activity improves the fitting of the modeled functional regions with the real observations, especially in data with high molecular identity, which recommends considering constraints on the protein activity in the development of substitution models of evolution.

Engineered cellulose nanofibers membranes with oppositely charge characteristics for high-performance salinity gradient power generation by reverse electrodialysis

Reverse electrodialysis (RED) using nanofluidic ion-selective membrane may convert the salinity difference between seawater and river water into electricity. However, heterogeneous modification reactions of cellulose commonly leads to the inhomogeneous distribution of surface charges, thereby hampering the improvement of cellulose-based nanofluidic membranes for energy conversion. Herein, RED devices based on cellulose nanofibers (CNF) membranes with opposite charge characteristics were developed for the generation of salinity gradient power. Anion-CNF membrane (A-CNF) with varying negative charge densities was synthesized using 2,2,6,6-Tetramethylpiperidine 1-oxy radical (TEMPO) oxidation modification, whereas cation-CNF membrane (C-CNF) was prepared through etherification. By mixing artificial seawater and river water, the output power density of CNF RED device is up to 2.87 W m-2. The output voltage of 30 RED units connected in series may reach up to 3.11 V, which can be used to directly power tiny electronic devices viz. LED lamp, calculator, etc. The results of this work provide a feasible possibility for widespread application of ion exchange membranes for salinity gradient energy harvesting.

Picking the lock of coordination cage catalysis

The design principles of metallo-organic assembly reactions have facilitated access to hundreds of coordination cages of varying size and shape. Many of these assemblies possess a well-defined cavity capable of hosting a guest, pictorially mimicking the action of a substrate binding to the active site of an enzyme. While there are now a growing collection of coordination cages that show highly proficient catalysis, exhibiting both excellent activity and efficient turnover, this number is still small compared to the vast library of metal-organic structures that are known. In this review, we will attempt to unpick and discuss the key features that make an effective coordination cage catalyst, linking structure to activity (and selectivity) using lessons learnt from both experimental and computational analysis of the most notable exemplars. We will also provide an outlook for this area, reasoning why coordination cages have the potential to become the gold-standard in (synthetic) non-covalent catalysis.

Fe3O4@ABA-aniline-CuI nanocomposite as a highly efficient and reusable nanocatalyst for the synthesis of benzothiazole-sulfide aryls and heteroaryls

Studying diaryl sulfides and benzothiazoles is important in organic synthesis because numerous natural and medicinal products contain these scaffolds. Over the past few years, research on the synthesis of compounds containing benzothiazole-sulfide aryls, as important biological molecules, has received significant attention. Multicomponent reactions are the most popular strategy for performing difficult reactions and the synthesis of complexed molecules such as benzothiazole-sulfide aryls. In this work, CuI was successfully immobilized on the surface of magnetic Fe₃O₄ nanoparticles modified with aniline and 4-aminobenzoic acid [Fe₃O₄@ABA-Aniline-CuI nanocomposite] and its catalytic activity was investigated in the preparation of a broad range of benzothiazole-sulfide aryls and heteroaryls through the one-pot three-component reactions of 2-iodoaniline with carbon disulfide and aryl or heteroaryl iodides in the presence of KOAc as base in PEG-400 as solvent. TEM and SEM images revealed that the shape of the Fe₃O₄@ABA-Aniline-CuI particles is spherical and the size of the particles is approximately between 12-25 nanometers.

Synthesis and electrochemical study of enzymatic graphene oxide-based nanocomposite as stable biosensor for determination of bevacizumab as a medicine in colorectal cancer in human serum and wastewater fluids

This work's goal was the fabrication of a graphene oxide-based nanocomposite biosensor for the determination of bevacizumab (BVZ) as a medicine for colorectal cancer in human serum and wastewater fluids. For the fabrication electrode, graphene oxide was electrodeposited on GCE (GO/GCE), and then DNA and monoclonal anti-bevacizumab antibodies were immobilized on the GO/GCE surface, respectively (Ab/DNA/GO/GCE). Structural characterization using XRD, SEM, and Raman spectroscopy confirmed the binding of DNA to GO nanosheets and the interaction of Ab with the DNA/GO array. Electrochemical characterization of Ab/DNA/GO/GCE using CV and DPV indicated immobilization of antibodies on DNA/GO/GCE and sensitive and selective behavior of modified electrodes for determination of BVZ. The linear range was obtained 10-1100 μg/mL, and the sensitivity and detection limit values were determined to be 0.14575 μA/μg.mL^-1 and 0.02 μg/mL, respectively. To verify the applicability of the planned sensor for determination of BVZ in human serum and wastewater fluid specimens, the outcomes of DPV measurements using Ab, DNA, GO, and GCE and the results of the Bevacizumab ELISA Kit for determination of BVZ in prepared real specimens showed good conformity between the outcomes of both analyses. Moreover, the proposed sensor showed considerable assay precision with recoveries ranging from 96.00% to 98.90% and acceptable relative standard deviations (RSDs) below 5.11%, illustrating sufficiently good sensor accuracy and validity in the determination of BVZ in prepared real specimens of human serum and wastewater fluids. These outcomes demonstrated the feasibility of the proposed BVZ sensor in clinical and environmental assay applications.

Kemp Eliminase Activity of Ketosteroid Isomerase

Kemp eliminases represent the most successful class of computationally designed enzymes, with rate accelerations of up to 10⁹-fold relative to the rate of the same reaction in aqueous solution. Nevertheless, several other systems such as micelles, catalytic antibodies, and cavitands are known to accelerate the Kemp elimination by several orders of magnitude. We found that the naturally occurring enzyme ketosteroid isomerase (KSI) also catalyzes the Kemp elimination. Surprisingly, mutations of D38, the residue that acts as a general base for its natural substrate, produced variants that catalyze the Kemp elimination up to 7000-fold better than wild-type KSI does, and some of these variants accelerate the Kemp elimination more than the computationally designed Kemp eliminases. Analysis of the D38N general base KSI variant suggests that a different active site carboxylate residue, D99, performs the proton abstraction. Docking simulations and analysis of inhibition by active site binders suggest that the Kemp elimination takes place in the active site of KSI and that KSI uses the same catalytic strategies of the computationally designed enzymes. In agreement with prior observations, our results strengthen the conclusion that significant rate accelerations of the Kemp elimination can be achieved with very few, nonspecific interactions with the substrate if a suitable catalytic base is present in a hydrophobic environment. Computational design can fulfill these requirements, and the design of more complex and precise environments represents the next level of challenges for protein design.

Regulation of protein-ligand binding affinity by hydrogen bond pairing

Hydrogen (H)-bonds potentiate diverse cellular functions by facilitating molecular interactions. The mechanism and the extent to which H-bonds regulate molecular interactions are a largely unresolved problem in biology because the H-bonding process continuously competes with bulk water. This interference may significantly alter our understanding of molecular function, for example, in the elucidation of the origin of enzymatic catalytic power. We advance this concept by showing that H-bonds regulate molecular interactions via a hitherto unappreciated donor-acceptor pairing mechanism that minimizes competition with water. On the basis of theoretical and experimental correlations between H-bond pairings and their effects on ligand binding affinity, we demonstrate that H-bonds enhance receptor-ligand interactions when both the donor and acceptor have either significantly stronger or significantly weaker H-bonding capabilities than the hydrogen and oxygen atoms in water. By contrast, mixed strong-weak H-bond pairings decrease ligand binding affinity due to interference with bulk water, offering mechanistic insight into why indiscriminate strengthening of receptor-ligand H-bonds correlates poorly with experimental binding affinity. Further support for the H-bond pairing principle is provided by the discovery and optimization of lead compounds targeting dietary melamine and Clostridium difficile toxins, which are not realized by traditional drug design methods. Synergistic H-bond pairings have therefore evolved in the natural design of high-affinity binding and provide a new conceptual framework to evaluate the H-bonding process in biological systems. Our findings may also guide wider applications of competing H-bond pairings in lead compound design and in determining the origin of enzymatic catalytic power.

BIOPHYSICS. Response to Comments on "Extreme electric fields power catalysis in the active site of ketosteroid isomerase"

Natarajan et al. and Chen and Savidge comment that comparing the electric field in ketosteroid isomerase's (KSI's) active site to zero overestimates the catalytic effect of KSI's electric field because the reference reaction occurs in water, which itself exerts a sizable electrostatic field. To compensate, Natarajan et al. argue that additional catalytic weight arises from positioning of the general base, whereas Chen and Savidge propose a separate contribution from desolvation of the general base. We note that the former claim is not well supported by published results, and the latter claim is intriguing but lacks experimental basis. We also take the opportunity to clarify some of the more conceptually subtle aspects of electrostatic catalysis.