Effect of Dextran 70 on the thermodynamic and structural properties of proteins

Deciphering the biophysical aspects of the interaction of 3,5,4'-trihydroxy-trans-stilbene with ribonuclease A: spectroscopic and computational studies

Drug-receptor interaction is an important aspect in drug action, drug discovery, and pharmacological aspects. The molecule 3,5,4'-trihydroxy-trans-stilbene known as resveratrol is a natural polyphenol and exhibits diverse biological activities. Ribonuclease A catalyses the degradation of RNA by its ribonucleolytic activity. The report presents the binding interaction of resveratrol with RNase A using experimental and theoretical techniques. Experimental studies revealed the interaction strength of 104 M-1 order with a single binding site. Resveratrol quenched the ribonuclease A fluorescence with a quenching constant of 104 M-1 range. The accessible fraction of the fluorophore was found to be 0.75 besides non-radiative energy transfer from ribonuclease A to resveratrol. The donor-acceptor distance was 2.14 nm from FRET calculations. No visible changes in the protein structure was evident from the circular dichroism studies. The interface residues involved in the interaction were obtained from docking studies. Further, the participation of the active site residues, His 12, His 119, and Lys 41 with interaction indicates the location of resveratrol near to the active site of ribonuclease A and indicates its possible potential to inhibit the ribonuclease A activity. The RMSD of less than 3 Å indicates stable conformation of protein in the complex. The protein RMSF value in the complex less than 3 Å shows no deviation of protein residues over time and thus suggests no conformational variation in the protein after binding.

Assessing Partial Inhibition of Ribonuclease A Activity by Curcumin through Fluorescence Spectroscopy and Theoretical Studies

Molecular interactions and controlled expression of enzymatic activities are fundamental to all cellular functions in an organism. The active polyphenol in turmeric known as curcumin (CCM) is known to exhibit diverse pharmacological activities. Ribonucleases (RNases) are the hydrolytic enzymes that plays important role in ribonucleic acid (RNA) metabolism. Uncontrolled and unwanted cleavage of RNA by RNases may be the cause of cell death leading to disease states. The protein ribonuclease A (RNase A) in the superfamily of RNases cleaves the RNA besides its role in different diseases like autoimmune diseases, and pancreatic disorders. Interaction of CCM with RNase A have been reported along with the possible role of CCM to inhibit the RNase A enzymatic activity. The interaction strength was found to be 104 M-1 order from spectroscopic results. Quenching of RNase A fluorescence by CCM was 104 M-1 order. Non-radiative energy transfer from RNase A (donor) to CCM (acceptor) suggested a distance of 2.42 nm between the donor-acceptor pair. Circular dichroism studies revealed no structural changes in RNase A after binding. Binding-induced conformational variation in protein was observed from synchronous fluorescence studies. Agarose gel electrophoresis revealed a partial inhibition of the RNase A activity by CCM though not significant. Molecular docking and molecular dynamics studies suggested the residues of RNase A involved in the interaction with supporting the experimental finding for the partial inhibition of the enzyme activity. This study may help in designing new CCM analogues or related structures to understand their differential inhibition of the RNase A activity.

Deeper Insights into Mixed Crowding through Enzyme Activity, Dynamics, and Crowder Diffusion

Given the fact that the cellular interior is crowded by many different kinds of macromolecules, it is important that in vitro studies be carried out in the presence of mixed crowder systems. In this regard, we have used binary crowders formed by the combination of some of the commonly used crowding agents, namely, Ficoll 70, Dextran 70, Dextran 40, and PEG 8000 (PEG 8), to study how these affect enzyme activity, dynamics, and crowder diffusion. The enzyme chosen is AK3L1, an isoform of adenylate kinase. To investigate its dynamics, we have carried out three single point mutations (A74C, A132C, and A209C) with the cysteine residues being labeled with a coumarin-based solvatochromic probe [CPM: (7-diethylamino-3-(4-maleimido-phenyl)-4-methylcoumarin)]. Both enzyme activity and dynamics decreased in the binary mixtures as compared with the sum of the individual crowders, suggesting a reduction in excluded volume (in the mixture). To gain deeper insights into the binary mixtures, fluorescence correlation spectroscopy studies were carried out using fluorescein isothiocyanate-labeled Dextran 70 and tetramethylrhodamine-labeled AK3L1 as the diffusion probes. Diffusion in binary mixtures was observed to be much more constrained (relative to the sum of the individual crowders) for the labeled enzyme as compared to the labeled crowder showing different environments being faced by the two species. This was further confirmed during imaging of the phase-separated droplets formed in the binary mixtures having PEG as one of the crowding agents. The interior of these droplets was found to be rich in crowders and densely packed, as shown by confocal and digital holographic microscopy images, with the enzymes predominantly residing outside these droplets, that is, in the relatively less crowded regions. Taken together, our data provide important insights into various aspects of the simplest form of mixed crowding, that is, composed of just two components, and also hint at the enhanced complexity that the cellular interior presents toward having a detailed and comprehensive understanding of the same.

Effects of Molecular Crowders on Single-Molecule Nucleic Acid Folding: Temperature-Dependent Studies Reveal True Crowding vs Enthalpic Interactions

Biomolecular folding in cells can be strongly influenced by spatial overlap/excluded volume interactions (i.e., "crowding") with intracellular solutes. As a result, traditional in vitro experiments with dilute buffers may not accurately recapitulate biomolecule folding behavior in vivo. In order to account for such ubiquitous excluded volume effects, biologically inert polyethylene glycol (PEG) and polysaccharides (dextran and Ficoll) are often used as in vitro crowding agents to mimic in vivo crowding conditions, with a common observation that high concentrations of these polymers stabilize the more compact biomolecule conformation. However, such an analysis can be distorted by differences in polymer interactions with the folded vs unfolded conformers, requiring temperature-dependent analysis of the thermodynamics to reliably assess competing enthalpic vs entropic contributions and thus the explicit role of excluded volume. In this work, temperature-controlled single-molecule fluorescence resonance energy transfer (smFRET) is used to characterize the thermodynamic interaction between nucleic acids and common polymer crowders PEG, dextran, and Ficoll. The results reveal that PEG promotes secondary and tertiary nucleic acid folding by simultaneously increasing the folding rate while decreasing the unfolding rate, with temperature-dependent studies confirming that the source of PEG stabilization is predominantly entropic and consistent with a true excluded volume crowding mechanism. By way of contrast, neither dextran nor Ficoll induces any significant concentration-dependent change in nucleic acid folding stability at room temperature, but instead, stabilization effects gradually appear with a temperature increase. Such a thermal response indicates that both folding enthalpies and entropies are impacted by dextran and Ficoll. A detailed thermodynamic analysis of the kinetics suggests that, instead of true entropic molecular crowding, dextran and Ficoll associate preferentially with the unfolded vs folded nucleic acid conformer as a result of larger solvent accessible surface area, thereby skewing the free energy landscapes through both significant entropic/enthalpic contributions that compete and fortuitously cancel near room temperature.

Crowding Milleu stabilizes apo-myoglobin against chemical-induced denaturation: Dominance of hardcore repulsions in the heme devoid protein

Macromolecular crowding can have significant consequences on the structure and dynamics of a protein. The size and shape of a co-solute molecule and the nature of protein contribute significantly in macromolecular crowding, which results in different outcomes in similar conditions. The structure of apo-myoglobin (apo-Mb) both in the absence and presence of denaturants (GdmCl and urea) was investigated in crowded conditions at pH 7.0, with a comparable size of crowders (~70 kDa) but of different shapes (ficoll and dextran) at various concentrations using spectroscopic techniques like absorption and circular dichroism to monitor changes in secondary and tertiary structure, respectively. The crowders in the absence of denaturants showed structural stabilization of the tertiary structure while no significant change in the secondary structure was observed. The effect of crowders on the stability of the protein was also investigated using probes such as Δε₂₉₁ and θ₂₂₂ using chemical denaturants. The analysis of chemical-induced denaturation curves showed that both the crowders stabilize apo-Mb by increasing the values of the midpoint of transition (C_m) and change in free energy in the absence of denaturant (∆G_D°), and it was observed that dextran 70 shows more stabilization than ficoll 70 under similar conditions. In this study apo-Mb showed stabilization under crowded conditions, which is a deviation from earlier work from our group where holo form of the same protein was destabilized. This study emphasizes that volume exclusion is a dominant force in a simple protein while soft interactions may play important role in the proteins that are possessing prosthetic group. Hence, the effect of crowders is protein-dependent, and excluded volume plays a great role in the stabilization of apo-Mb, which does not interact with the crowders.

Interactions Under Crowding Milieu: Chemical-Induced Denaturation of Myoglobin is Determined by the Extent of Heme Dissociation on Interaction with Crowders

Generally, in vivo function and structural changes are studied by probing proteins in a dilute solution under in vitro conditions, which is believed to be mimicking proteins in intracellular milieu. Earlier, thermal-induced denaturation of myoglobin, in the milieu of crowder molecule showed destabilization of the metal protein. Destabilization of protein by thermal-induced denaturation involves a large extrapolation, so, the reliability is questionable. This led us to measure the effects of macromolecular crowding on its stability by chemical-induced denaturation of the protein using probes like circular dichroism and absorption spectroscopy in the presence of dextran 70 and ficoll 70 at various pHs (acidic: 6.0, almost neutral: 7.0 and basic: 8.0). Observations showed that the degree of destabilization of myoglobin was greater due to ficoll 70 as compared to that of dextran 70 so it can be understood that the nature of the crowder or the shape of the crowder has an important role towards the stability of proteins. Additionally, the degree of destabilization was observed as pH dependent, however the pH dependence is different for different crowders. Furthermore, isothermal titration calorimetry and molecular docking studies confirmed that both the crowders (ficoll and dextran) bind to heme moiety of myoglobin and a single binding site was observed for each.

Carbohydrate-Based Macromolecular Crowding-Induced Stabilization of Proteins: Towards Understanding the Significance of the Size of the Crowder

There are a large number of biomolecules that are accountable for the extremely crowded intracellular environment, which is totally different from the dilute solutions, i.e., the idealized conditions. Such crowded environment due to the presence of macromolecules of different sizes, shapes, and composition governs the level of crowding inside a cell. Thus, we investigated the effect of different sizes and shapes of crowders (ficoll 70, dextran 70, and dextran 40), which are polysaccharide in nature, on the thermodynamic stability, structure, and functional activity of two model proteins using UV-Vis spectroscopy and circular dichroism techniques. We observed that (a) the extent of stabilization of α-lactalbumin and lysozyme increases with the increasing concentration of the crowding agents due to the excluded volume effect and the small-sized and rod-shaped crowder, i.e., dextran 40 resulted in greater stabilization of both proteins than dextran 70 and ficoll 70; (b) structure of both the proteins remains unperturbed; and (c) enzymatic activity of lysozyme decreases with the increasing concentration of the crowder.

Mixture of Macromolecular Crowding Agents Has a Non-additive Effect on the Stability of Proteins

The folding and unfolding of proteins inside a cell take place in the presence of macromolecules of various shapes and sizes. Such crowded conditions can significantly affect folding, stability, and biophysical properties of proteins. Thus, to logically mimic the intracellular environment, the thermodynamic stability of two different proteins (lysozyme and α-lactalbumin) was investigated in the presence of mixtures of three crowding agents (ficoll 70, dextran 70, and dextran 40) at different pH values. These crowders possess different shapes and sizes. It was observed that the stabilizing effect of mixtures of crowders is more than the sum effects of the individual crowder, i.e., the stabilizing effect is non-additive in nature. Moreover, dextran 40 (in the mixture) has been found to exhibit the greatest stabilization when compared with other crowders in the mixture. In other words, the small size of the crowder has been observed to be a dominant factor in stabilization of the proteins. Graphical Abstract.

Making microenvironments: A look into incorporating macromolecular crowding into in vitro experiments, to generate biomimetic microenvironments which are capable of directing cell function for tissue engineering applications

Biomimetic microenvironments are key components to successful cell culture and tissue engineering in vitro. One of the most accurate biomimetic microenvironments is that made by the cells themselves. Cell-made microenvironments are most similar to the in vivo state as they are cell-specific and produced by the actual cells which reside in that specific microenvironment. However, cell-made microenvironments have been challenging to re-create in vitro due to the lack of extracellular matrix composition, volume and complexity which are required. By applying macromolecular crowding to current cell culture protocols, cell-made microenvironments, or cell-derived matrices, can be generated at significant rates in vitro. In this review, we will examine the causes and effects of macromolecular crowding and how it has been applied in several in vitro systems including tissue engineering.

Crowding interactions perturb structure and stability by destabilizing the stable core of the α-subunit of tryptophan synthase

The consequences of crowding derived from relatively small and intrinsically disordered proteins are not clear yet. We report the effect of ficoll-70 on the structure and stability of native and partially folded states of the 29 kDa alpha subunit of tryptophan synthase (αTS). Overall, combining the changes in the circular dichroism and fluorescence spectra, in conjunction with the gradual loss of cooperativity under urea denaturation in the presence of increasing amounts of ficoll, it may be concluded that the crowding agent perturbs not only the native state but also the partially folded state of αTS. Importantly, NMR data indicate that ficoll interacts with the residues that constitute the stable core of the protein thus shedding light on the origin of the observed perturbation.

Relationship between protein stability and functional activity in the presence of macromolecular crowding agents alone and in mixture: An insight into stability-activity trade-off

The cellular environment is crowded with different kinds of molecules with varying sizes, shapes and compositions. Most of the experiments studying the nature and behaviour of a protein have been done on the isolated protein in dilute buffer solutions which actually do not imitate the in vivo situation. To understand the consequences of such crowded environment, we investigated the effect of macromolecular crowding on the stability and activity of hen egg white lysozyme. Two crowding agents, dextran 70 and ficoll 70 which have different shapes and composition, have been employed in this study. To mimic the cellular condition from physiological point of view, the effect of mixtures of both the crowding agents has been also studied. The results indicate that owing to volume exclusion, lysozyme is stabilized while its activity decays with the increasing concentration of both the crowders elucidating the hypothesis of stability-activity trade-off. Mixed macromolecular crowding exerts greater effect than the sum of constituent crowding agents (dextran 70 and ficoll 70).