Thermodynamic principle to enhance enzymatic activity using the substrate affinity

Free-energy transduction mechanisms shape the flux space of metabolic networks

The transduction of free energy in metabolic networks represents a thermodynamic mechanism by which the free energy derived from nutrients is converted to drive nonspontaneous, energy-requiring metabolic reactions. This transduction is typically observed in processes that generate energy-rich molecules such as ATP and NAD(P)H, which, in turn, power specific reactions, particularly biosynthetic reactions. This property establishes a pivotal connection between the intricate topology of metabolic networks and their ability to redirect energy for functional purposes. The present study proposes a dedicated framework aimed at exploring the relationship between free-energy dissipation, network topology, and metabolic objectives. The starting point is that, regardless of the network topology, nonequilibrium chemostatting conditions impose stringent thermodynamic constraints on the feasible flux steady states to satisfy energy and entropy balances. An analysis of randomly sampled reaction networks shows that the network topology imposes additional constraints that restrict the accessible flux solution space, depending on key structural features such as the reaction's molecularity, reaction cycles, and conservation laws. Notably, topologies featuring multimolecular reactions that implement free-energy transduction mechanisms tend to extend the accessible flux domains, facilitating the achievement of metabolic objectives such as anabolic flux maximization or flux rerouting capacity. This approach is applied to a coarse-grained model of carbohydrate metabolism, highlighting the structural requirements for optimal biomass yield.

Significantly enhanced specific activity of Bacillus subtilis (2,3)-butanediol dehydrogenase through computer-aided refinement of its substrate-binding pocket

(2,3)-Butanediol dehydrogenases (BDHs) are widely utilized for the stereoselective interconversion between α-hydroxy ketones and vicinal diols to produce various functional building blocks. In this study, to enhance the specific activity towards (R)-phenyl-1,2-ethanediol (1a) for 2-hydroxyacetophenone (1b), the substrate-binding pocket of a Bacillus subtilis BDH (BsBDHA) was refined through site-directed mutagenesis. Based on molecular docking simulations, 14 residues were identified and subjected to alanine scanning mutagenesis. After screening, two residues, His42 and Gly292, were singled out for partial site-saturation mutagenesis. The results revealed that BsBDHAH42A and BsBDHAG292A displayed high activities of 3.21 and 1.97 U/mg, respectively. Employing combinatorial mutagenesis, a superior mutant, BsBDHAI49L/V266L/G292A, was developed, exhibiting significantly enhanced specific activity and catalytic efficiency towards (R)-1a, achieving 14.81 U/mg and 4.47 mM-1 s-1, respectively, which were 27.4- and 55.9-fold higher than those of BsBDHA. Further substrate spectrum analysis revealed that the superior mutant displayed increased specific activities for (R)-2a-6a by 1.4- to 10.3-fold. The integration of BsBDHAI49L/V266L/G292A into a three-enzymatic cascade for the synthesis of 1b effectively elevated the yield from 58.1 to 82.4%. Molecular mechanism analysis indicated that the mutation-induced changes in intermolecular forces resulted in a higher frequency of reactive conformations for (R)-1a in BsBDHAI49L/V266L/G292A compared to BsBDHA.

Bioreceptor modified electrochemical biosensors for the detection of life threating pathogenic bacteria: a review

The lack of reliable and efficient techniques for early monitoring to stop long-term effects on human health is an increasing problem as the pathogenesis effect of infectious bacteria is growing continuously. Therefore, developing an effective early detection technique coupled with efficient and continuous monitoring of pathogenic bacteria is increasingly becoming a global public health prime target. Electrochemical biosensors are among the strategies that can be utilized for accomplishing that goal with promising potential. In recent years, identifying target biological analytes by interacting with bioreceptors modified electrodes is among the most commonly used detection techniques in electrochemical biosensing strategies. The commonly employed bioreceptors are nucleic acid molecules (DNA or RNA), proteins, antibodies, enzymes, organisms, tissues, and biomimetic components such as molecularly imprinted polymers. Despite the advancement in electrochemical biosensing, developing a reliable and effective biosensor for detecting pathogenic bacteria is still in the infancy stage with so much room for growth. A major milestone in addressing some of the issues and improving the detection pathway is the investigation of specific bacterial detection techniques. The present study covers the fundamental concepts of electrochemical biosensors, human PB illnesses, and the latest electrochemical biosensors based on bioreceptor elements that are designed to detect specific pathogenic bacteria. This study aims to assist researchers with the most up-to-date research work in the field of bio-electrochemical pathogenic bacteria detection and monitoring.

Directed-evolution mutations enhance DNA-binding affinity and protein stability of the adenine base editor ABE8e

Adenine base editors (ABEs), consisting of CRISPR Cas nickase and deaminase, can chemically convert the A:T base pair to G:C. ABE8e, an evolved variant of the base editor ABE7.10, contains eight directed evolution mutations in its deaminase TadA8e that significantly increase its base editing activity. However, the functional implications of these mutations remain unclear. Here, we combined molecular dynamics (MD) simulations and experimental measurements to investigate the role of the directed-evolution mutations in the base editing catalysis. MD simulations showed that the DNA-binding affinity of TadA8e is higher than that of the original deaminase TadA7.10 in ABE7.10 and is mainly driven by electrostatic interactions. The directed-evolution mutations increase the positive charge density in the DNA-binding region, thereby enhancing the electrostatic attraction of TadA8e to DNA. We identified R111, N119 and N167 as the key mutations for the enhanced DNA binding and confirmed them by microscale thermophoresis (MST) and in vivo reversion mutation experiments. Unexpectedly, we also found that the directed mutations improved the thermal stability of TadA8e by ~ 12 °C (Tm, melting temperature) and that of ABE8e by ~ 9 °C, respectively. Our results demonstrate that the directed-evolution mutations improve the substrate-binding ability and protein stability of ABE8e, thus providing a rational basis for further editing optimisation of the system.

Revealing isochoric water nucleation: a visual study

The phenomena of water freezing at constant volume, or isochoric, is becoming more and more fascinating. However, because the system is subjected to extremely high pressures, it is exceedingly challenging to investigate it visually. Fewer properties have been found visually up till now, but many have been found through other means. Nevertheless, we were able to design a reactor so that it could be observed through a microscope as water was frozen and thawed at constant volume, reaching temperatures as low as - 12 °C and pressures up to 129 MPa. In this study, we observed critical characteristics visually, focusing on the location of the ice nucleus, its shape, and dynamics. Phase transitions from liquid to solid state are essential mechanisms in the physical sciences. The creation of ice stands as the quintessential and pervasive example of nucleation, playing a central role in diverse disciplines such as geology, biology, aviation, and climate research.

Rationalizing the Influence of the Binding Affinity on the Activity of Phosphoserine Phosphatases

The Sabatier principle states that catalytic activity can be maximized when the substrate binding affinity is neither too strong nor too weak. Recent studies have shown that the activity of several hydrolases is maximized at intermediate values of the binding affinity (Michaelis-Menten constant: Km ). However, it remains unclear whether this concept of artificial catalysis is applicable to enzymes in general, especially for those which have evolved under different reaction environments. Herein, we show that the activity of phosphoserine phosphatase is also enhanced at an intermediate Km value of approximately 0.5 mM. Within our dataset, the variation of Km by three orders of magnitude accounted for a roughly 18-fold variation in the activity. Owing to the high phylogenetic and physiological diversity of our dataset, our results support the importance of optimizing Km for enzymes in general. On the other hand, a 77-fold variation in the activity was attributed to other physicochemical parameters, such as the Arrhenius prefactor of kcat , and could not be explained by the Sabatier principle. Therefore, while tuning the binding affinity according to the Sabatier principle is an important consideration, the Km value is only one of many physicochemical parameters which must be optimized to maximize enzymatic activity.

Bioluminescence of (R)-Cypridina Luciferin with Cypridina Luciferase

Cypridina luciferin (CypL) is a marine natural product that functions as the luminous substrate for the enzyme Cypridina luciferase (CypLase). CypL has two enantiomers, (R)- and (S)-CypL, due to its one chiral center at the sec-butyl moiety. Previous studies reported that (S)-CypL or racemic CypL with CypLase produced light, but the luminescence of (R)-CypL with CypLase has not been investigated. Here, we examined the luminescence of (R)-CypL, which had undergone chiral separation from the enantiomeric mixture, with a recombinant CypLase. Our luminescence measurements demonstrated that (R)-CypL with CypLase produced light, indicating that (R)-CypL must be considered as the luminous substrate for CypLase, as in the case of (S)-CypL, rather than a competitive inhibitor for CypLase. Additionally, we found that the maximum luminescence intensity from the reaction of (R)-CypL with CypLase was approximately 10 fold lower than that of (S)-CypL with CypLase, but our kinetic analysis of CypLase showed that the Km value of CypLase for (R)-CypL was approximately 3 fold lower than that for (S)-CypL. Furthermore, the chiral high-performance liquid chromatography (HPLC) analysis of the reaction mixture of racemic CypL with CypLase showed that (R)-CypL was consumed more slowly than (S)-CypL. These results indicate that the turnover rate of CypLase for (R)-CypL was lower than that for (S)-CypL, which caused the less efficient luminescence of (R)-CypL with CypLase.