Denaturation and Preservation of Globular Proteins: The Role of DMSO

Self-Reporting Therapeutic Protein Nanoparticles

We present a modular strategy to synthesize nanoparticle sensors equipped with dithiomaleimide-based, fluorescent molecular reporters capable of discerning minute changes in interparticle chemical environments based on fluorescence lifetime analysis. Three types of nanoparticles were synthesized with the aid of tailor-made molecular reporters, and it was found that protein nanoparticles exhibited greater sensitivity to changes in the core environment than polymer nanogels and block copolymer micelles. Encapsulation of the hydrophobic small-molecule drug paclitaxel (PTX) in self-reporting protein nanoparticles induced characteristic changes in fluorescence lifetime profiles, detected via time-resolved fluorescence spectroscopy. Depending on the mode of drug encapsulation, self-reporting protein nanoparticles revealed pronounced differences in their fluorescence lifetime signatures, which correlated with burst- vs diffusion-controlled release profiles observed in previous reports. Self-reporting nanoparticles, such as the ones developed here, will be critical for unraveling nanoparticle stability and nanoparticle-drug interactions, informing the future development of rationally engineered nanoparticle-based drug carriers.

Relationship Between Cryoprotectant Potential and Protein Hydration in Aqueous Zwitterionic Solutions

The cryoprotectant potential of 3-(1-(2-(2-methoxyethoxy)ethyl)imidazol-3-io)butane-1-carboxylate (OE2imC3C) for proteins necessitates assessment to elucidate its relationship with protein hydration. To reveal this relationship, we assessed the protein stability (pre-freezing and post-thawing) and melting behavior in dilute aqueous protein-OE2imC3C solutions containing varying mole fractions (x) of OE2imC3C (x = 0, 7.7 × 10-3, and 1.7 × 10-2) using Fourier-transform infrared (FTIR) and near-UV circular dichroism (near-UV CD) spectroscopy and differential scanning calorimetry (DSC) techniques. Following freezing/thawing using a deep freezer, protein stability in aqueous OE2imC3C solutions (x = 1.7 × 10-2) preserved the folded state owing to the protein-OE2imC3C interaction, whereas stability at x = 7.7 × 10-3 was reduced. These results indicate that the protein cryoprotectant potential in aqueous OE2imC3C solutions at x = 1.7 × 10-2 is higher than that at x = 7.7 × 10-3, owing to the preferential binding of OE2imC3C with proteins.

DMSO-Related Effects on Ligand-Binding Properties of Lysine Methyltransferases G9a and SETD8

Being the standard solvent for preparing stock solutions of compounds for drug discovery, DMSO is always present in assay buffers in concentrations ranging from 0.1 % to 5 % (v/v). Even at the lowest concentrations, DMSO-containing solutions can have significant effects on individual proteins and possible pitfalls cannot be eliminated. Herein, we used two protein systems, the lysine methyltransferases G9a/KMT1 C and SETD8/KMT5 A, to study the effects of DMSO on protein stability and on the binding of the corresponding inhibitors, using different biophysical methods such as nano Differential Scanning Fluorimetry (nanoDSF), Differential Scanning Fluorimetry (DSF), microscale thermophoresis (MST), and surface plasmon resonance (SPR), all widely used in drug discovery screening campaigns. We demonstrated that the effects of DMSO are protein- and technique-dependent and cannot be predicted or extrapolated on the basis of previous studies using different proteins and/or different assays. Moreover, we showed that the application of orthogonal biophysical methods can lead to different binding affinity data, thus confirming the importance of using at least two different orthogonal assays in screening campaigns. This variability should be taken into account in the selection and characterization of hit compounds, in order to avoid data misinterpretation.

Redefining the Molecular Interplay between Dimethyl Sulfoxide, Lipid Bilayers, and Dehydration

The potentially damaging action of dimethyl sulfoxide (DMSO) on phospholipid bilayers remains a matter of controversy. We have conducted a series of long-scale molecular dynamics simulations of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers at various levels of hydration in the presence of variable quantities of DMSO. These simulations provide evidence for a non-destructive dehydrating mechanism of action for DMSO on DOPC bilayers across a wide concentration range and levels of hydration. Specifically, under full- and low-hydration conditions, the bilayer underwent a minor lateral contraction, coinciding with surface dehydration in the presence of dilute DMSO solutions (X_DMSO < 0.3). At higher DMSO concentrations, this bilayer structure was retained despite a progressive deterioration of the hydration structure at the interface. A similar convergence of bilayer structural properties was observed under dehydration conditions for 0.3 < X_DMSO < 0.7. Destabilization occurred for dehydrated bilayers in the presence of X_DMSO ≥ 0.7, suggesting the existence of a DMSO concentration and/or dehydration threshold. However, such DMSO concentrations far exceed those established as toxic to other cellular components. Our findings represent a computational model for DMSO-DOPC interactions that is consistent with a range of experimental characterizations, offering new molecular insights into the cryoprotective mechanisms of action of DMSO.

The incipient denaturation mechanism of DNA

DNA denaturation is related to many important biological phenomena, such as its replication, transcription and the interaction with some specific proteins for single-stranded DNA. Dimethyl sulfoxide (DMSO) is a common chemical agent for DNA denaturation. In the present study, we investigate quantitatively the effects of different concentrations of DMSO on plasmid and linear DNA denaturation by atomic force microscopy (AFM) and UV spectrophotometry. We found that persistent length of DNA decreases significantly by adding a small amount of DMSO before ensemble DNA denaturation occurs; the persistence length of DNA in 3% DMSO solution decreases to 12 nm from about 50 nm without DMSO in solution. And local DNA denaturation occurs even at very low DMSO concentration (such as 0.1%), which can be directly observed in AFM imaging. Meanwhile, we observed the forming process of DNA contacts between different parts for plasmid DNA with increasing DMSO concentration. We suggest the initial mechanism of DNA denaturation as follows: DNA becomes more flexible due to the partial hydrogen bond braking in the presence of DMSO before local separation of the two complementary nucleotide chains.

The persistent length of DNA decreases significantly by adding small amount of DMSO. Local DNA denaturation occurs even at very low DMSO concentration, which can be observed by atomic force microscopy directly.

Amyloid Self-Assembly of Lysozyme in Self-Crowded Conditions: The Formation of a Protein Oligomer Hydrogel

A method is designed to quickly form protein hydrogels, based on the self-assembly of highly concentrated lysozyme solutions in acidic conditions. Their properties can be easily modulated by selecting the curing temperature. Molecular insights on the gelation pathway, derived by in situ FTIR spectroscopy, are related to calorimetric and rheological results, providing a consistent picture on structure–property correlations. In these self-crowded samples, the thermal unfolding induces the rapid formation of amyloid aggregates, leading to temperature-dependent quasi-stationary levels of antiparallel cross β-sheet links, attributed to kinetically trapped oligomers. Upon subsequent cooling, thermoreversible hydrogels develop by the formation of interoligomer contacts. Through heating/cooling cycles, the starting solutions can be largely recovered back, due to oligomer-to-monomer dissociation and refolding. Overall, transparent protein hydrogels can be easily formed in self-crowding conditions and their properties explained, considering the formation of interconnected amyloid oligomers. This type of biomaterial might be relevant in different fields, along with analogous systems of a fibrillar nature more commonly considered.

Heat-induced self-assembling of BSA at the isoelectric point

Materials based on ordered protein aggregates have recently received a lot of attention for their application as drug carriers, due to their biocompatibility and their ability to sequester many biological fluids. Bovine serum albumin (BSA) is a good candidate for this use due to its high availability and tendency to aggregate and gel under acidic conditions. In the present work, we employ spectroscopic techniques to investigate the heat-induced BSA aggregation at the molecular scale, in the 12-84 °C temperature range, at pH = 5 where two different isoforms of the protein are stable. Samples at low and high protein concentration are examined. With the advantage of the combined use of FTIR and CD, we recognize the aggregation-prone species and the different distribution of secondary structures, conformational rearrangements and types of aggregates, of millimolar compared to micromolar BSA solutions. Further, as a new tool, we use the Maximum Entropy Method to fit the kinetic curves to investigate the distribution of kinetic constants of the complex hierarchical aggregation process. Finally, we characterize the activation energy of the initial self-assembling step to observe that the formation of both small and large aggregates is driven by the same interactions.

Ultrafast Dynamics at the Lipid-Water Interface: DMSO Modulates H-Bond Lifetimes

Dimethyl sulfoxide (DMSO) is a common cosolvent and cryopreservation agent used to freeze cells and tissues. DMSO alters the H-bond structure of water, but its interactions with biomolecules and, specifically, with biological interfaces remain poorly understood. Here we investigate the effects of DMSO on the H-bond dynamics at the lipid-water interface using a combination of ultrafast two-dimensional infrared (2D IR) spectroscopy and molecular dynamics simulations. Ester carbonyl absorption spectra show that DMSO dehydrates the interface, and simulations show that the area per lipid is decreased. Ultrafast 2D IR spectra measure the time scales of frequency fluctuations at the ester carbonyl positions located precisely between the hydrophobic and hydrophilic regions of the membrane. 2D IR measurements show that low DMSO concentrations (<10 mol %) induce ∼40% faster H-bond dynamics compared with pure water, whereas increased concentrations (>10-20 mol %) once again slow down the dynamics. This slow-fast-slow trend is described in terms of two different solvation regimes. Below 10 mol %, DMSO weakens the interfacial H bond, leading to faster "bulk-like" dynamics, whereas above 10 mol %, water molecules become "relatively immobilized" as the H-bond networks becoming disrupted by the H-bond donor/acceptor imbalance at the interface. These studies are an important step toward characterizing the environments around lipid membranes, which are essential to numerous biological processes.

The Effect of Dimethyl Sulfoxide on the Lysozyme Unfolding Kinetics, Thermodynamics, and Mechanism

The thermal stability of proteins in the presence of organic solvents and the search for ways to increase this stability are important topics in industrial biocatalysis and protein engineering. The denaturation of hen egg-white lysozyme in mixtures of water with dimethyl sulfoxide (DMSO) with a broad range of compositions was studied using a combination of differential scanning calorimetry (DSC), circular dichroism (CD), and spectrofluorimetry techniques. In this study, for the first time, the kinetics of unfolding of lysozyme in DMSO–water mixtures was characterized. In the presence of DMSO, a sharp decrease in near-UV CD and an increase in the fluorescence signal were observed at lower temperatures than the DSC denaturation peak. It was found that differences in the temperatures of the CD and DSC signal changes increase as the content of DMSO increases. Changes in CD and fluorescence are triggered by a break of the tertiary contacts, leading to an intermediate state, while the DSC peak corresponds to a subsequent complete loss of the native structure. In this way, the commonly used two-state model was proven to be unsuitable to describe the unfolding of lysozyme in the presence of DMSO. In kinetic studies, it was found that even high concentrations of DMSO do not drastically change the activation energy of the initial stage of unfolding associated with a disruption of the tertiary structure, while the enthalpy of denaturation shows a significant dependence on DMSO content. This observation suggests that the structure of the transition state upon unfolding remains similar to the structure of the native state.

Effects of aprotic solvents on the stability of metal-free superoxide dismutase probed by native electrospray ionization-ion mobility-mass spectrometry

Considering that aprotic solvents are often used as cosolvents in investigating the interactions between small molecules and proteins, we assessed the effects of five aprotic solvents represented by dimethylformamide (DMF) on the structure stabilities of metal-free SOD1 (apo-SOD1) by native electrospray ionization-ion mobility-mass spectrometry (ESI-IM-MS). These aprotic solvents include DMF, 1,3-dimethyl-2-imidazolidinone (DMI), dimethyl sulfoxide (DMSO), acetonitrile (ACN), and tetrahydrofuran (THF). Results indicated that DMI, DMSO, and DMF at low percentage concentration could reduce the average charge and the dimer dissociation of apo-SOD1. By contrast, ACN and THF at low concentration have no similar effect. DMF was selected as a representative solvent to further investigate the detailed effects on the structure stability of apo-SOD1 by using collision-induced dissociation and unfolding. The results reveal that the addition of minimal DMF to an aqueous protein solution can protect against the unfolding and dissociation of dimer, even under destabilizing conditions (such as low pH or high cone voltage). When the different percentage concentrations of DMF were added, the average collision cross section of apo-SOD1 showed that apo-SOD1 became compacted when the DMF concentration increased from 0% to 1% and eventually started extending when increased from 1% to 20%. The results indicated that DMF has similar effects to DMSO in native mass spectrometry (MS) and it can also be used as a cosolvent besides DMSO in investigating the stabilities of proteins and the interactions between small molecules and proteins.

Probing Globular Protein Self-Assembling Dynamics by Heterodyne Transient Grating Experiments

In this work, we studied the propagation of ultrasonic waves of lysozyme solutions characterized by different degrees of aggregation and networking. The experimental investigation was performed by means of the transient grating (TG) spectroscopy as a function of temperature, which enabled measurement of the ultrasonic acoustic proprieties over a wide time window, ranging from nanoseconds to milliseconds. The fitting of the measured TG signal allowed the extraction of several dynamic properties, here we focused on the speed and the damping rate of sound. The temperature variation induced a series of processes in the lysozyme solutions: Protein folding-unfolding, aggregation and sol–gel transition. Our TG investigation showed how these self-assembling phenomena modulate the sound propagation, affecting both the velocity and the damping rate of the ultrasonic waves. In particular, the damping of ultrasonic acoustic waves proved to be a dynamic property very sensitive to the protein conformational rearrangements and aggregation processes.

Scrutiny of electrostatic-driven conformational ordering of polypeptide chains in DMSO: a study with a model oligopeptide

The molecular mechanism of DMSO-induced stabilisation of β-sheets is attributed to the combination of polar electrostatic interactions among side chains, and backbone desolvation through bulky side chains which promotes backbone hydrogen bonding.

Investigation of DMSO-induced conformational transitions in human serum albumin using two-dimensional raman optical activity spectroscopy

Recent Raman and Raman optical activity (ROA) results have demonstrated that dimethyl sulfoxide (DMSO) induces the selective conversion of α-helix motifs into the poly(L-proline) II (PPII) helix conformation in an array of proteins, while β-sheets remain mostly unaffected. Human serum albumin (HSA), a highly α-helical protein, underwent the most dramatic changes and, therefore, was selected as a model for further investigations into the mechanism of this conformational change. Herein we report the use of two-dimensional ROA correlation analysis applying synchronous, autocorrelation, and moving windows approaches in order to understand the conformational transitions in HSA as a function of DMSO concentration. Our results indicate that the destabilization of native α-helix starts at DMSO concentrations as little as 20% in water (v/v), with the transition to PPII helix being complete at ~80% DMSO. These results clearly indicate that any protein preparation containing relatively low concentrations of DMSO should consider possible disruptions in α-helical domains.

Simplicity within the complexity: bilateral impact of DMSO on the functional and unfolding patterns of α-chymotrypsin

New understanding of the fundamental links between protein stability, conformational flexibility and function, can be gained through synergic studies on their catalytic and folding/unfolding properties under the influence of stabilizing/destabilizing additives. We explored an impact of dimethyl sulfoxide (DMSO), the moderate effector of multilateral action, on the kinetic (functional) and thermodynamic (thermal unfolding) patterns of a hydrolytic enzyme, α-chymotrypsin (α-CT), over a wide range of additive concentrations, 0-70% (v/v). Both the calorimetric and kinetic data exhibited rich behavior pointing to the complex interplay of global/local stability (and flexibility) patterns. The complex action of DMSO is explained through the negative and positive preferential solvation motifs that prevail for the extreme opposite, native-like and unfolded states, respectively, implying essential stabilization of compact domains by enhancement of interfacial water networks and destabilization of a flexible active site by direct binding of DMSO to the unoccupied specific positions intended for elongated polypeptide substrates.