Multifaceted folding-unfolding landscape of the TrpZip2 β-hairpin and the role of external sub-piconewton mechanical tensions

Proteins can experience uneven tensions of the order of tens of piconewtons when exposed to different solvent environment due to the thermal motion of the solvent. It is also true that biomolecules, especially proteins, are subjected to a variety of mechanical tensions generated by several factors, including mechanically assisted translocation and pressure gradients within living systems. Here, we use metadynamics simulations to revisit the folding-unfolding of the TrpZip2 β-hairpin and redefine it from the perspective of an external force of a sub-piconewton magnitude acting on the ends of the hairpin. The chosen forces, while preserving the morphology of the β-hairpin chain when it is pulled, are capable of influencing the conformational behavior of the chain during folding and unfolding. Our investigations confirm that the TrpZip2 β-hairpin exhibits a zipper (zip-out) mechanism for folding-unfolding in both mechanically unbiased and biased (with a 30 pN end force) situations. However, it is important to note that they present marked differences in their folding and unfolding paths, with the mechanically biased system capable of becoming trapped in various intermediate states. Both unbiased and biased scenarios of the hairpin indicate that the hairpin turn is highly stable during the folding-unfolding event and initiates folding. More importantly we confirm that the existing heterogeneity in the TrpZip2 β-hairpin folding-unfolding is a consequence of the wide range of conformations observed, owing to the different trapped intermediates caused by the uneven forces it may experience in solution.

Towards solvent regulated self-activation of N-terminal disulfide bond oxidoreductase-D

N-terminal disulfide bond oxidoreductase-D (nDsbD), an essential redox enzyme in Gram-negative bacteria, consists of a single disulfide bond (Cys₁₀₃-Cys₁₀₉) in its active site. The enzymatic functions are believed to be regulated by an electron transfer mediated redox switching of the disulfide bond, which is vital in controlling bacterial virulence factors. In light of the disulfide bond's inclination towards nucleophilic cleavage, it is also plausible that an internal nucleophile could second the existing electron transfer mechanism in nDsbD. Using QM/MM MD metadynamics simulations, we explore different possibilities of generating an internal nucleophile near the nDsbD active site, which could serve as a fail-over mechanism in cleaving the disulfide bond. The simulations show the formation of the internal nucleophile Tyr₄₂O^- (F ≈ 9 kcal mol^-1) and its stabilization through the solvent medium. The static gas-phase calculations show that Tyr₄₂O^- could be a potential nucleophile for cleaving the S-S bond. Most strikingly, it is also seen that Tyr₄₂O^- and Asp₆₈OH communicate with each other through a proton-hole like water wire (F ≈ 12 kcal mol^-1), thus modulating the nucleophile formation. Accordingly, we propose the role of a solvent in regulating the internal nucleophilic reactions and the subsequent self-activation of nDsbD. We believe that this could be deterministic while designing enzyme-targeted inhibitor compounds.

Highly Selective Entrapment of His-Tagged Enzymes on Superparamagnetic Zirconium-Based MOFs with Robust Renewability to Enhance pH and Thermal Stability

Metal-organic frameworks (MOFs), as a kind of poriferous nanoparticle, are promising candidates for enzyme immobilization to enhance their stability and reusability. However, most MOFs could not specifically immobilize enzymes and regenerate easily, which inevitably leads to serious high consumption and environmental pollution. In this study, renewable and magnetic MOFs were first constructed to specially immobilize His-tagged enzymes from the cell lysates without purification. The immobilized β-glucuronidase exhibited wider pH adaptability and temperature stability. The relative activity of immobilized β-glucuronidase was still maintained at ∼80% after eight cycles. Importantly, after simple treatment, the immobilization capacity of regenerated MOFs after simple treatment was restored to more than 90% in the first three times. The specific magnetic MOFs were proven to be an efficient and renewable platform for one-step immobilization and purification of His-tagged enzymes, showing great potential in industrial applications of nanotechnology and biocatalysis.