Enzyme Active Site Loop Revealed as a Gatekeeper for Cofactor Flip by Targeted Molecular Dynamics Simulations and FRET-Based Kinetics

Assessing the impact of choline chloride and benzyltrimethylammonium chloride-based deep eutectic solvents on the structure and conformational dynamics of bovine serum albumin: a combined steady-state, time-resolved fluorescence and fluorescence correlation spectroscopic study

Although deep eutectic solvents (DESs) are regarded as useful substitutes for both ionic liquids and common organic solvents for storage and applications of biomolecules, it is still unclear whether all DESs or only specific types of DESs will be suitable for the said purpose. In view of this, the current study aims to report on the structure and conformational dynamics of BSA in the presence of two DESs, namely ethaline (choline chloride:ethylene glycol) and BMEG (benzyltrimethyl ammonium chloride:ethylene glycol), having the same hydrogen bond donor but with a distinct hydrogen bond acceptor, so that how small changes in one constituent of a DES alter the protein-DES interaction at the molecular level can be understood. The protein-DES interaction is investigated by exploiting both ensemble-averaged measurements like steady-state and time-resolved fluorescence spectroscopy, circular dichroism (CD) spectroscopy, and single-molecule sensitive techniques based on fluorescence correlation spectroscopy (FCS). Interestingly, the results obtained from these studies have demonstrated that while a very small quantity of BMEG completely unfolds the native structure of the protein, it remains in a partially unfolded state even at very high ethaline content. More interestingly, it has been found that at very high concentrations of BMEG, the unfolded protein undergoes enhanced protein-protein interaction resulting in the aggregation of BSA. All of the results obtained from these investigations have essentially suggested that both protein-DES interaction and interspecies interaction among the constituent of DESs play a crucial role in governing the overall stability and conformational dynamics of the protein in DESs.

Engineering Embden-Meyerhof-Parnas Glycolysis to Generate Noncanonical Reducing Power

Noncanonical cofactors such as nicotinamide mononucleotide (NMN+) supplant the electron-transfer functionality of the natural cofactors, NAD(P)+, at a lower cost in cell-free biomanufacturing and enable orthogonal electron delivery in whole-cell metabolic engineering. Here, we redesign the high-flux Embden-Meyerhof-Parnas (EMP) glycolytic pathway to generate NMN+-based reducing power, by engineering Streptococcus mutans glyceraldehyde-3-phosphate dehydrogenase (Sm GapN) to utilize NMN+. Through iterative rounds of rational design, we discover the variant GapN Penta (P179K-F153S-S330R-I234E-G210Q) with high NMN+-dependent activity and GapN Ortho (P179K-F153S-S330R-I234E-G214E) with ~3.4 × 106-fold switch in cofactor specificity from its native cofactor NADP+ to NMN+. GapN Ortho is further demonstrated to function in Escherichia coli only in the presence of NMN+, enabling orthogonal control of glucose utilization. Molecular dynamics simulation and residue network connectivity analysis indicate that mutations altering cofactor specificity must be coordinated to maintain the appropriate degree of backbone flexibility to position the catalytic cysteine. These results provide a strategy to guide future designs of NMN+-dependent enzymes and establish the initial steps toward an orthogonal EMP pathway with biomanufacturing potential.

Molecular Dynamics Analysis of a Rationally Designed Aldehyde Dehydrogenase Gives Insights into Improved Activity for the Non-Native Cofactor NAD

The aldehyde dehydrogenase from Thermoplasma acidophilum was previously implemented as a key enzyme in a synthetic cell-free reaction cascade for the production of alcohols. In order to engineer the enzyme's cofactor specificity from NADP⁺ to NAD⁺, we identified selectivity-determining residues with the CSR-SALAD tool and investigated further positions based on the crystal structure. Stepwise combination of the initially discovered six point mutations allowed us to monitor the cross effects of each mutation, resulting in a final variant with reduced K_M for the non-native cofactor NAD⁺ (from 18 to 0.6 mM) and an increased activity for the desired substrate d-glyceraldehyde (from 0.4 to 1.5 U/mg). Saturation mutagenesis of the residues at the entrance of the substrate pocket could eliminate substrate inhibition. Molecular dynamics simulations showed a significant gain of flexibility at the cofactor binding site for the final variant. The concomitant increase in stability against isobutanol and only a minor reduction in its temperature stability render the final variant a promising candidate for future optimization of our synthetic cell-free enzymatic cascade.

Dynamics of a Key Conformational Transition in the Mechanism of Peroxiredoxin Sulfinylation

Peroxiredoxins from the Prx1 subfamily (Prx) are moonlighting peroxidases that operate in peroxide signaling and are regulated by sulfinylation. Prxs offer a major model of protein–thiol oxidative modification. They react with H₂O₂ to form a sulfenic acid intermediate that either engages into a disulfide bond, committing the enzyme into its peroxidase cycle, or again reacts with peroxide to produce a sulfinic acid that inactivates the enzyme. Sensitivity to sulfinylation depends on the kinetics of these two competing reactions and is critically influenced by a structural transition from a fully folded (FF) to locally unfolded (LU) conformation. Analysis of the reaction of the Tsa1 Saccharomyces cerevisiae Prx with H₂O₂ by Trp fluorescence-based rapid kinetics revealed a process linked to the FF/LU transition that is kinetically distinct from disulfide formation and suggested that sulfenate formation facilitates local unfolding. Use of mutants of distinctive sensitivities and of different peroxide substrates showed that sulfinylation sensitivity is not coupled to the resolving step kinetics but depends only on the sulfenic acid oxidation and FF-to-LU transition rate constants. In addition, stabilization of the active site FF conformation, the determinant of sulfinylation kinetics, is only moderately influenced by the Prx C-terminal tail dynamics that determine the FF → LU kinetics. From these two parameters, the relative sensitivities of Prxs toward hyperoxidation with different substrates can be predicted, as confirmed by in vitro and in vivo patterns of sulfinylation.