Region-Specific Double Denaturation of Human Serum Albumin: Combined Effects of Temperature and GnHCl on Structural and Dynamical Responses

Understanding the intricacy of protein in hydrated deep eutectic solvent: Solvation dynamics, conformational fluctuation dynamics, and stability

Deep eutectic solvents (DESs) are potential biocatalytic media due to their easy preparation, fine-tuneability, biocompatibility, and most importantly, due to their ability to keep protein stable and active. However, there are many unanswered questions and gaps in our knowledge about how proteins behave in these alternate media. Herein, we investigated solvation dynamics, conformational fluctuation dynamics, and stability of human serum albumin (HSA) in 0.5 Acetamide/0.3 Urea/0.2 Sorbitol (0.5Ac/0.3Ur/0.2Sor) DES of varying concentrations to understand the intricacy of protein behaviour in DES. Our result revealed a gradual decrease in the side-chain flexibility and thermal stability of HSA beyond 30 % DES. On the other hand, the associated water dynamics around domain-I of HSA decelerate only marginally with increasing DES content, although viscosity rises considerably. We propose that even though macroscopic solvent properties are altered, a protein feels only an aqueous type of environment in the presence of DES. This is probably the first experimental study to delineate the role of the associated water structure of the enzyme for maintaining its stability inside DES. Although considerable effort is necessary to generalize such claims, it might serve as the basis for understanding why proteins remain stable and active in DES.

Explanation of inconsistencies in the determination of human serum albumin thermal stability

Thermal denaturation of human serum albumin has been the subject of many studies in recent decades, but the results of these studies are often conflicting and inconclusive. To clarify this, we combined different spectroscopic and calorimetric techniques and performed an in-depth analysis of the structural changes that occur during the thermal unfolding of different conformational forms of human serum albumin. Our results showed that the inconsistency of the results in the literature is related to the different quality of samples in different batches, methodological approaches and experimental conditions used in the studies. We confirmed that the presence of fatty acids (FAs) causes a more complex process of the thermal denaturation of human serum albumin. While the unfolding pathway of human serum albumin without FAs can be described by a two-step model, consisting of subsequent reversible and irreversible transitions, the thermal denaturation of human serum albumin with FAs appears to be a three-step process, consisting of a reversible step followed by two consecutive irreversible transitions.

Applications of fluorescence spectroscopy in protein conformational changes and intermolecular contacts

Emission fluorescence is one of the most versatile and powerful biophysical techniques used in several scientific subjects. It is extensively applied in the studies of proteins, their conformations, and intermolecular contacts, such as in protein-ligand and protein-protein interactions, allowing qualitative, quantitative, and structural data elucidation. This review, aimed to outline some of the most widely used fluorescence techniques in this area, illustrate their applications and display a few examples. At first, the data on the intrinsic fluorescence of proteins is disclosed, mainly on the tryptophan side chain. Predominantly, research to study protein conformational changes, protein interactions, and changes in intensities and shifts of the fluorescence emission maximums were discussed. Fluorescence anisotropy or fluorescence polarization is a measurement of the changing orientation of a molecule in space, concerning the time between the absorption and emission events. Absorption and emission indicate the spatial alignment of the molecule's dipoles relative to the electric vector of the electromagnetic wave of excitation and emitted light, respectively. In other words, if the fluorophore population is excited with vertically polarized light, the emitted light will retain some polarization based on how fast it rotates in solution. Therefore, fluorescence anisotropy can be successfully used in protein-protein interaction investigations. Then, green fluorescent proteins (GFPs), photo-transformable fluorescent proteins (FPs) such as photoswitchable and photoconvertible FPs, and those with Large Stokes Shift (LSS) are disclosed in more detail. FPs are potent tools for the study of biological systems. Their versatility and wide range of colours and properties allow many applications. Finally, the application of fluorescence in life sciences is exposed, especially the application of FPs in fluorescence microscopy techniques with super-resolution that enables precise in vivo photolabeling to monitor the movement and interactions of target proteins.

Introducing the multi-dimensional spectral phasors: a tool for the analysis of fluorescence excitation-emission matrices

The use of phasors to analyze fluorescence data was first introduced for time-resolved studies for a simpler mathematical analysis of the fluorescence-decay curves. Recently, this approach was extended to steady-state experiments with the introduction of the spectral phasors (SP), derived from the Fourier transform of the fluorescence emission spectrum. In this work, we revise key mathematical aspects that lead to an interpretation of SP as the characteristic function of a probability distribution. This formalism allows us to introduce a new tool, called multi-dimensional spectral phasor (MdSP) that seize, not only the information from the emission spectrum, but from the full excitation-emission matrix (EEM). In addition, we developed a homemade open-source Java software to facilitate the MdSP data processing. Due to this mathematical conceptualization, we settled a mechanism for the use of MdSP as a tool to tackle spectral signal unmixing problems in a more accurate way than SP. As a proof of principle, with the use of MdSP we approach two important biophysical questions: protein conformational changes and protein-ligand interactions. Specifically, we experimentally measure the EEM changes upon denaturation of human serum albumin (HSA) or during its association with the fluorescence dye 1,8-anilinonaphtalene sulphate (ANS) detected via tryptophan-ANS Förster Resonance Energy Transfer (FRET). In this sense, MdSP allows us to obtain information of the system in a simpler and finer way than the traditional SP. Specifically, understanding a protein's EEM as a molecular fingerprint opens new doors for the use of MdSP as a tool to analyze and comprehend protein conformational changes and interactions.

Macromolecular Crowding Effect on the Structure, Function, Conformational Dynamics and Relative Domain Movement of a Multi-Domain Protein as a function of Crowder Shape and Interaction

The cellular environment is crowded by macromolecules of various sizes, shapes, and charges, which modulate protein structure, function and dynamics. Herein, we contemplated the effect of three different macromolecular crowders:...

Plasma Protein Binding of Herbal-Flavonoids to Human Serum Albumin and Their Anti-proliferative Activities

Herbal-flavonoids (HF) as polyphenolic secondary metabolites are taken in the daily diet to join in many metabolic processes in the human organism. Anti-proliferative activities and human serum albumin (HSA) binding capacities of herbal-flavonoids namely 7,5'-dimethoxyisoetin (HF1), homoorientin-6''-4-O-methyl-myo-inositol (HF2), (2R, 3R)-(+)-dihydrokaempferol-7,4'-dimethylether (HF3), eriodictyol-7,4'-dimethylether (HF4) and flavonoids isoorientin (HF5) and genkwanin (HF6) were investigated. Anti-proliferative activities were determined by the xCELLigence system by treatment with human prostate (PC3) and cervical cancer (HeLa) cells. The binding capacities were studied by two-dimensional (2D-FL) and three-dimensional (3D-FL) fluorescence spectroscopy. HeLa and PC3 cell lines were treated with flavonoids at 10, 50 and 100 μg/mL concentrations over a 48 hour period. Stable anti-proliferative efficacy plots were obtained for tested flavonoids. From the flavonoids, HF3 and HF4 showed the strongest anti-proliferative effect against PC3 and HeLa cell line. HF1 and HF2 exhibited the strongest binding capacity to the HSA corresponding to Kb values of 3.81 x 104 M-1 and 6.00 x 104 M-1, respectively. The studies revealed that the flavonoids form the basis of in vivo preclinical studies as important nutraceuticals of the daily diet, as well as modelled in medical and pharmacological applications.

Domain-Specific Stabilization of Structural and Dynamic Responses of Human Serum Albumin by Sucrose

Background:

Human Serum Albumin (HSA) is the most abundant protein present in human blood plasma. It is a large multi-domain protein with 585 amino acid residues. Due to its importance in human body, studies on the interaction of HSA with different external agent is of vital interest. The denaturation and renaturation of HSA in presence of external agents are of particular interest as they affect the biological activity of the protein.

Objective:

The objective of this work is to study the domain-specific and overall structural and dynamical changes occurring to HSA in the presence of a denaturing agent, urea and a renaturing agent, sucrose.

Methods:

In order to carry out the domain-specific studies, HSA has been tagged using N-(7- dimethylamino-4-methylcoumarin-3-yl) iodoacetamide (DACIA) at Cys-34 of domain-I and pnitrophenyl coumarin ester (NPCE) at Tyr-411 site in domain-III, separately. Steady-state absorption, emission and solvation dynamic measurements have been carried out in order to monitor the domain-specific alteration of HSA caused by the external agents. The overall structural change of HSA have been monitored using circular dichroism spectroscopy.

Results:

The α-helicity of HSA was found to decrease from 65% to 11% in presence of urea and was found to further increase to 25% when sucrose is added, manifesting the denaturing and renaturing effects of urea and sucrose, respectively. The steady state studies show that domain-III is more labile towards denaturation as compared to domain-I. The presence of an intermediate state is observed during the denaturation process. The stabilization of this intermediate state in presence of sucrose is attributed as the reason for the stabilization of HSA by sucrose. From solvation dynamics studies, it could be seen that the solvation time of DACIA inside domain-I of HSA decreases and increases regularly with increasing concentrations of urea and sucrose, respectively, while in the case of NPCE-tagged domain-III, the effect of sucrose on solvation time is evident only at high concentrations of urea.

Conclusion:

The denaturing and renaturing effects of urea and sucrose could be clearly seen from the steady state studies and circular dichroism spectroscopy measurements. A regular change in solvation time could only be observed in the case of domain-I and not in domain-III. The results indicate that the renaturing effect of sucrose on domain-III is not very evident when protein is in its native state, but is evident in when the protein is denatured.</P>

Spectroscopic Insight on Ethanol-Induced Aggregation of Papain

In this contribution, the structural and dynamic changes occurring to papain in ethanol-water binary solvent mixtures have been investigated and compared with its denatured state. Steady-state fluorescence, solvation dynamics, time-resolved rotational anisotropy, circular dichroism (CD), and single molecular-level fluorescence correlation spectroscopic (FCS) studies were performed for this purpose. In ethanol-water mixtures with X_EtOH = 0.6, N-(7-dimethylamino-4-methylcoumarin-3-yl)iodoacetamide (DACIA)-tagged papain was found to undergo a blue shift of 12 nm, while in the presence of 5 M GnHCl, a red shift of 5 nm was observed. Solvation dynamics of the system was also found to be different in the presence of these external agents. In ethanol-water mixtures, the average solvation time was found to increase almost 2-fold as compared to that in water, while in the presence of GnHCl, only a marginal increase could be observed. These changes of DACIA-tagged papain in ethanol-water mixtures are attributed to the aggregation of the protein in the presence of ethanol. The residual anisotropy was found to increase 14-fold, and the rotational time component corresponding to the rotation of the probe molecule was found to increase by 4-fold in the ethanol-water mixture which also gives a notion of the papain aggregation. Atomic force microscopy (AFM) confirms this aggregate formation, which is also quantified by the FCS study. The hydrodynamic radius of the protein aggregates in ethanol-water mixtures was calculated to be ∼155 Å as compared to the corresponding value of 18.4 Å in the case of native monomer papain. Also, it confirmed that the aggregate formation takes place even in the nanomolar concentration of papain. Analysis of circular dichroism spectra of papain showed that an increase in the β-sheet content of papain at the expense of α-helix and the random coil with an increase of the ethanol mole fraction may be responsible for this aggregation process.