Dodine as a protein denaturant: the best of two worlds?

Polygonum odoratum essential oil inhibits the activity of mushroom derived tyrosinase

Plant derived compounds are a source of long term research focus due to their applications in a variety of fields, particularly food preservation. One key way in which phytochemicals are crucial in this area is by disrupting enzyme functionality. In this work, essential oil was extracted by steam distillation from the fresh leaves of Polygonum odoratum (Polygonaceae), commonly known as Vietnamese coriander, and shown to effectively inhibit the oxidation of L-3,4-dihydroxyphenylalanine (L-DOPA) catalyzed by mushroom tyrosinase (EC1.14.18.1). Using GC-MS analysis, twenty five compounds were identified in the essential oil. The most abundant compounds in the essential oil were Alkanals - dodecanal (55.49%), and decanal (11.57%) - followed by anisaldehyde (6.35%); these compounds were individually investigated for inhibitory activity by performing single-compound screening. Each of the top three most abundant compounds inhibited the tyrosinase-catalyzed oxidation of L-DOPA, as identified by UV-VIS spectroscopy and oxygen consumption assays. The inhibitory activity of the major compounds increased when pre-incubated with tyrosinase and without significant additional oxygen consumption, suggesting k_cat-type inactivation is not involved. Interactions of the head and tail components of the major alkanals may disrupt the tertiary structure of the enzyme, presenting a potential inhibitory mechanism.

Does Fungicide "Dodine" Unfold Protein like Kosmo-Chaotropic Agent?

The nontargeted action of fungicides affects the structure of protein, which leads to several serious diseases such as nausea, cancer, fetus malformations, movement dysfunction, and behavioral changes in human and animals. Hence, understanding of the structural change in protein induced by fungicides is of utmost importance to decode its mode of nontargeted action. In this study, we have investigated the structural change of myoglobin by an important fungicide, namely, dodine (n-dodecylguanidinium acetate), as well as its analogues n-hexylguanidinium acetate (HGA) and guanidinium chloride (GdmCl) using spectroscopic and thermodynamic methods. The amount of dodine and HGA required for the unfolding of myoglobin is significantly less than GdmCl. GdmCl, dodine, and HGA unfold the myoglobin by decreasing the content of the helical and tertiary structures. However, the decrease in the content of tertiary structure is significantly higher than that of the secondary structure for dodine and HGA, in contrast to GdmCl, where the decrease in secondary and tertiary contents of protein is not biased. Thermodynamic and spectroscopic data depict that the unfolding of the dodine and HGA is driven by the hydrophobic interaction, whereas the hydrogen bonding of GdmCl with the amino acids of protein plays a key role in the unfolding. The long alkyl chain of dodine and HGA get accommodated at the surface of the helices of myoglobin, inducing strong hydrophobic interaction, which causes its unfolding. This study depicts that dodine unfolds protein by the chaotropic effect in which its hydrocarbon chain destabilizes the protein by the hydrophobic effect, unlike in an earlier study, where dodine was claimed to be a kosmo-chaotropic agent as its hydrocarbon group stabilizes the protein.

Dodine as a Kosmo-Chaotropic Agent

Denaturants such as the guanidinium cation unfold proteins at molar concentrations, which interferes with ultraviolet- and infrared-based spectroscopy measurements. Dodine denatures some proteins cooperatively at a thousand-fold lower concentration, allowing for spectroscopy measurements. Nonetheless, dodine's microscopic mechanism of interaction with proteins is not understood. We probe the effect of dodine on α-helices and tertiary structure by investigating the stability of the small helical protein B. Experiments show that dodine promotes formation of helical structure (a kosmotropic effect), while inducing the loss of tertiary structure (a chaotropic effect). Although dodine destabilizes native protein structure, it does not lower the thermal denaturation midpoint temperature of protein B. All-atom simulations reveal the cause for both observations: The denaturant action of dodine's guanidyl headgroup is counteracted by its aliphatic tail, which stabilizes amphipathic helices and associates with an expanded protein core. The Janus-like behavior of headgroup and tail make dodine a simultaneous stabilizer-destabilizer or "kosmo-chaotrope".

Molecular dynamics approach to understand the denaturing effect of a millimolar concentration of dodine on a λ-repressor and counteraction by trehalose

Here, we use a molecular dynamics approach to calculate the spatial distribution function of the ternary water–dodine–trehalose (1.0 M) system.

Dodine as a transparent protein denaturant for circular dichroism and infrared studies

The fungicide dodine combines the cooperative denaturation properties of guanidine with the mM denaturation activity of SDS. It was previously tested only on two small model proteins. Here we show that it can be used as a chemical denaturant for phosphoglycerate kinase (PGK), a much larger two-domain enzyme. In addition to its properties as a chemical denaturant, dodine facilitates thermal denaturation of PGK, and we show for the first time that it also facilitates pressure denaturation of a protein. Much higher quality circular dichroism and amide I' infrared spectra of PGK can be obtained in dodine than in guanidine, opening the possibility for use of dodine as a denaturant when UV or IR detection is desirable. One caution is that dodine denaturation, like other detergent-based denaturants, is less reversible than guanidine denaturation.

The Effect of Fluorescent Protein Tags on Phosphoglycerate Kinase Stability Is Nonadditive

It is frequently assumed that fluorescent protein tags used in biological imaging experiments are minimally perturbing to their host protein. As in-cell experiments become more quantitative and measure rates and equilibrium constants, rather than just "on-off" activity or the presence of a protein, it becomes more important to understand such perturbations. One criterion for a protein modification to be a perturbation is additivity of two perturbations (a linear effect on the protein free energy). Here we show that adding fluorescent protein tags to a host protein in vitro has a large nonadditive effect on its folding free energy. We compare an unlabeled, three singly labeled, and a doubly labeled enzyme (phosphoglycerate kinase). We propose two mechanisms for nonadditivity. In the "quinary interaction" mechanism, two tags interact transiently with one another, relieving the host protein from unfavorable tag-protein interactions. In the "crowding" mechanism, adding two tags provides the minimal crowding necessary to overcome destabilizing interactions of individual tags with the host protein. Both of these mechanisms affect protein stability in cells; we show here that they must also be considered for tagged proteins used for reference in vitro.

Comparing Fast Pressure Jump and Temperature Jump Protein Folding Experiments and Simulations

The unimolecular folding reaction of small proteins is now amenable to a very direct mechanistic comparison between experiment and simulation. We present such a comparison of microsecond pressure and temperature jump refolding kinetics of the engineered WW domain FiP35, a model system for β-sheet folding. Both perturbations produce experimentally a faster and a slower kinetic phase, and the "slow" microsecond phase is activated. The fast phase shows differences between perturbation methods and is closer to the downhill limit by temperature jump, but closer to the transiently populated intermediate limit by pressure jump. These observations make more demands on simulations of the folding process than just a rough comparison of time scales. To complement experiments, we carried out several pressure jump and temperature jump all-atom molecular dynamics trajectories in explicit solvent, where FiP35 folded in five of the six simulations. We analyzed our pressure jump simulations by kinetic modeling and found that the pressure jump experiments and MD simulations are most consistent with a 4-state kinetic mechanism. Together, our experimental and computational data highlight FiP35's position at the boundary where activated intermediates and downhill folding meet, and we show that this model protein is an excellent candidate for further pressure jump molecular dynamics studies to compare experiment and modeling at the folding mechanism level.