Molecular dynamics of structural effects of reactive carbonyl species derivate of lipid peroxidation on bovine serum albumin

BACKGROUND

Serum albumin is the most abundant protein in the Mammalia blood plasma at where plays a decisive role in the transport wide variety of hydrophobic ligands. BSA undergoes oxidative modifications like the carbonylation by the reactive carbonyl species (RCSs) 4-hydroxy-2-nonenal (HNE), 4 hydroxy-2-hexenal (HHE), malondialdehyde (MDA) and 4-oxo-2-nonenal (ONE), among others. The structural and functional changes induced by protein carbonylation have been associated with the advancement of neurodegenerative, cardiovascular, metabolic and cancer diseases.

METHODS

To elucidate structural effects of protein carbonylation with RCSs on BSA, parameters for six new non-standard amino acids were designated and molecular dynamics simulations of its mono‑carbonylated-BSA systems were conducted in the AMBER force field. Trajectories were evaluated by RMSD, RMSF, PCA, RoG and SASA analysis.

RESULTS

An increase in the conformational instability for all proteins modified with local changes were observed, without significant changes on the BSA global three-dimensional folding. A more relaxed compaction level and major solvent accessible surface area for modified systems was found. Four regions of high molecular fluctuation were identified in all modified systems, being the subdomains IA and IIIB those with the most remarkable local conformational changes. Regarding essential modes of domain movements, it was evidenced that the most representatives were those related to IA subdomain, while IIIB subdomain presented discrete changes.

CONCLUSIONS

RCSs induces local structural changes on mono‑carbonylated BSA. Also, this study extends our knowledge on how carbonylation by RCSs induce structural effects on proteins.

Counteraction Effects of Ammonium-Based Ionic Liquids on Urea-Induced Denaturation of α-Lactalbumin: A Comprehensive Molecular Simulation Study

Ionic liquids (ILs) are known to stabilize protein conformations in aqueous medium. Importantly, ILs can also act as refolding additives in urea-driven denaturation of proteins. However, despite the importance of the problem, detailed microscopic understanding of the counteraction effects of ILs on urea-induced protein denaturation remains elusive. In this work, atomistic molecular dynamics (MD) simulations of the protein α-lactalbumin have been carried out in pure aqueous medium, in 8 M binary urea-water solution and in ternary urea-IL-water solutions containing ammonium-based ethyl ammonium acetate (EAA) as the IL at different concentrations (1-4 M). Attempts have been made to quantify detailed molecular-level understanding of the origin behind the counteraction effects of the IL on urea-induced partial unfolding of the protein. The calculations revealed significant conformational changes of the protein with multiple free energy minima due to its partial unfolding in binary urea-water solution. The counteraction effect of the IL was evident from the enhanced structural rigidity of the protein with propensity to transform into a single native free energy minimum state in ternary urea-IL-water solutions. Such an effect has been found to be associated with preferential direct binding of the IL components with the protein and simultaneous expulsion of urea from the interface, thereby providing additional stabilization of the protein in ternary solutions. Most importantly, modified rearrangement of the hydrogen bond network at the interface due to the formation of stronger protein-cation (PC) and protein-anion (PA) hydrogen bonds by breaking relatively weaker protein-urea (PU) and protein-water (PW) hydrogen bonds has been recognized as the microscopic origin behind the counteraction effects of EAA on urea-induced partial unfolding of the protein.

2-Phenylquinoline-polyamine conjugate (QPC): Interaction with bovine serum albumin (BSA)

A novel 2-phenylquinoline-polyamine conjugate (QPC) was synthesized and characterized, its interaction with bovine serum albumin (BSA) was evaluated using UV-Vis, fluorescence and circular dichroism (CD) spectroscopy. The results showed that QPC caused a whole train of spectral variation, including enhancement of UV-vis absorption and reduction of fluorescence (FL), indicating QPC-BSA complex formed. FL results showed that the type of FL quenching waslarge static quenching, which was also accompanied with a process of dynamic quenching. Binding constants, thermodynamic parameters and docking results showed that the interaction between QPC and BSA was basically a Van der Waals, hydrogen bond and hydrophobic interaction. Synchronous and 3D-FL analysis revealed that QPC resulted in unapparent conformational alteration of BSA. The docking study suggested QPC was situated at the binding sites II of BSA, and 2-phenylquinoline moiety contributed to the hydrophobic interaction. The results of molecular dynamics revealed QPC altered the conformation of BSA, which showed that the inconsistency between experimental data and theoretical calculation results may be due to the instability of the compound.

Probing the interaction between niobium pentoxide nanoparticles and serum albumin proteins by Spectroscopic approaches

Nanoparticles (NPs) can directly or indirectly enter into the body because of their small size; then they tend to alter the conformation and function of proteins upon interaction with them. Thus, it is crucial to understand the impact of NPs in a biological medium. Recently, niobium pentoxide nanoparticles (Nb2O5 NPs) are finding increasing applications in the biological system, for example, bone tissue and dental material, matrix for biosensing of proteins, etc. In all such applications, the Nb2O5 NP interacts with proteins and other biomolecules. Hence, the study of such interactions is of considerable importance. Here in this work, we present the impact of Nb2O5 NP on the structure, stability and activity of blood proteins, bovine serum albumin (BSA) and human serum albumin (HSA) by means of various spectroscopic approaches. Steady-state fluorescence studies indicated that intrinsic fluorescence intensities of both serum albumin proteins got quenched upon their interaction with NP. The nature of the quenching was elucidated by time-resolved fluorescence and absorption measurements. Using circular dichroism (CD) and synchronous fluorescence spectroscopy (SFS), the structural perturbations of the protein molecules after interaction with NP were investigated. Moreover, the role of temperature on protein stability upon complexation with NP was also explored. In addition, the effect of NP on protein functionality was probed by esterase-like activity assays.Communicated by Ramaswamy H. Sarma.

The impact of Zn doping on CdTe quantum dots-protein corona formation and the subsequent toxicity at the molecular and cellular level

Understanding the formation of protein corona (PC) is of vital importance for exploring the toxicity of nanoparticles and promoting their safe applications. In this study, CdTe QDs doping with 0, 1%, 5% and 10% Zn were synthesized using one-pot hydrothermal methods. Afterwards, this study explored and compared the formation of pure and Zn doped-QDs PC as well as the subsequent molecular and cellular toxicity. Result found that Zn doping regulated the toxicity of Cd-QDs by controlling their ability to adsorb serum proteins. The adsorption to Cd-QDs induced the dispersion, unfolding, secondary structural changes and the activity loss of bovine serum albumin (BSA). Among the synthesized Cd-QDs, 10%Zn-QDs exhibited the highest fluorescence quantum yield and lowest molecular toxicity. The formations of pure QDs and 10%Zn-QDs with BSA corona are majorly driven by different forces with different patterns. The regulation of BSA on the cytotoxicity differences of pure QDs and 10%Zn-QDs was similar with fetal bovine serum, proving the significant contribution of BSA to the cytotoxicity of Cd-QDs PC. Compared with pure QDs PC, the higher cytotoxicity and oxidative stress level of 10%Zn-QDs PC were correlated with higher intracellular [Cd²⁺]. Both larger amount of BSA adsorption and higher level of intracellular reactive oxygen species could accelerate the dissolution rates of 10%Zn-QDs and thus result in higher intracellular [Cd²⁺].

An Overview on the Recent Advances in Alternative Solvents as Stabilizers of Proteins and Enzymes

Currently, the use of alternative solvents is increasing, namely ionic liquids (ILs) and deep eutectic solvents (DESs) in diverse fields of knowledge, such as biochemistry, chemistry, chemical engineering, biotechnology and biomedicine. Particularly, when compared to traditional solvents, these alternative solvents have great importance for biomolecules due to the enhanced solubility, structure stability and the biological activity of biomolecules, such as protein and enzymes. Thus, in this review article, the recent developments and efforts on the technological developments carried out with ILs and DESs for the stabilization and activation of proteins and enzymes are provided. The most studied IL- and DES-based formulations for proteins and enzymes are discussed and the molecular mechanisms and interactions related to the increased stability promoted by these alternative solvents are disclosed, while emphasizing their main advantages.

Multi-Spectroscopic, thermodynamic and molecular docking studies to investigate the interaction of eplerenone with human serum albumin

The binding of small molecular drugs with human serum albumin (HSA) has a crucial influence on their pharmacokinetics. The binding interaction between the antihypertensive Eplerenone (EPL)and HSA was investigated using multi-spectroscopic techniques for the first time. These techniques include UV-Vis spectroscopy, Fourier Transform Infrared (FT-IR), native fluorescence spectroscopy, synchronous fluorescence spectroscopy and molecular docking approach. The fluorescence spectroscopic study showed that EPL quenched HSA inherent fluorescence. The mechanism for quenching of HSA by EPL has been determined to be static in nature and confirmed by UV absorption and fluorescence spectroscopy. The modified Stern-Volmer equation was used to estimate the binding constant (K_b ) as well as the number of bindings (n). The results indicated that the binding occurs at a single site (Kb;2.238 x 10³ L mol^-1 at 298 K). The enthalpy and entropy changes (∆H and ∆S) were 58.061 and 0.258 K J mol^-1 , respectively, illustrating that the principal intermolecular interactions stabilizing the EPL-HSA system are hydrophobic forces. Synchronous fluorescence spectroscopy revealed that EPL binding to HSA occurred around the tyrosine residue (Tyr) and this agreed with the molecular docking study. The FRET analysis confirmed the static quenching mechanism. The esterase enzyme activity of HSA was also evaluated showing its decrease in the presence of EPL. Furthermore, docking analysis and site-specific markers experiment revealed that EPL binds with HSA at subdomain IB (site III).

Structural adaptations in the bovine serum albumin protein in archetypal deep eutectic solvent reline and its aqueous mixtures

The global concern over the environmental impact and challenges associated with the use of conventional solvents in biotransformation processes have pushed the search for alternative solvents. Recently, deep eutectic solvents (DESs) have appeared as a promising replacement with better biocompatibility and have been postulated to hold great potential in protein engineering and crystallization processes. In this context, herein, we have investigated the effect of reline (a choline chloride : urea mixture in 1 : 2 proportion) DES in its pure and hydrated forms on the structural stability and conformation of the bovine serum albumin (BSA) protein using all-atom molecular dynamics simulations. We observe a substantial overall expansion of the BSA structure with a simultaneous increment in the solvent accessible surface area, signifying the influence of reline on the BSA tertiary structure. These induced structural perturbations are quite pronounced in reline-water mixtures. Concomitantly, a notable reline concentration-dependent disruption of the BSA secondary structure through the melting of α-helices, mainly driven by H-bonding interactions, is observed. In the presence of pure reline, significant rigidity in the protein backbone is also observed. Thus, despite the expansion, the BSA tertiary structure in pure reline is found to be most close to the native protein structure and remains in a partially folded state at all the studied reline concentrations. In pure reline, BSA-urea hydrogen bonding is more prevalent than BSA-[Ch]⁺. We also observe that in aqueous reline systems, the BSA-water hydrogen bonds are mostly compensated by BSA-urea hydrogen bonds. The aqueous re-equilibration of these partially denatured protein conformations showed a significant recovery of secondary and tertiary structures, where the recovery is most profound for the BSA conformation extracted from pure reline.

Contrasting Effects of Ionic Liquids of Varying Degree of Hydrophilicity on the Conformational and Interfacial Properties of a Globular Protein

Ionic liquids (ILs), depending on their cation-anion combinations, are known to influence the conformational properties and activities of proteins in a nonuniform manner. To obtain microscopic understanding of such influence, it is important to characterize protein-IL interactions and explore the modified solvation environment around the protein. In this work, molecular dynamics (MD) simulations of the globular protein α-lactalbumin have been carried out in aqueous IL solutions containing 1-butyl-3-methylimidazolium cations (BMIM⁺) in combination with a series of anions with varying degree of hydrophilicity, namely, hexafluorophosphate (PF₆^-), ethyl sulfate (ETS^-), acetate (OAc^-), chloride (Cl^-), dicyanamide (DCA^-), and nitrate (NO₃^-) . The calculations revealed that ILs with hydrophobic and hydrophilic anions have contrasting influence on conformational flexibility of the protein. It is further observed that the BMIM⁺ cations exhibit site-specific orientations at the interface depending on the hydrophilicity of the anion component. Most importantly, the results demonstrated enhanced propensity of hydrophilic ILs to replace relatively weaker protein-water hydrogen bonds by stronger protein-IL hydrogen bonds at the protein surface as compared to the hydrophobic ILs. Such breaking of protein-water hydrogen bonds at a greater extent leads to greater loss of water hydrating the protein in the presence of hydrophilic ILs, thereby reducing the protein's stability.

Polyethylene glycol perturbs the unfolding of CRABP I: A correlation between experimental and theoretical approach

The importance of macromolecules paves the way towards a detailed molecular level investigation as all most all cellular processes occurring at the interior of cells in the form of proteins, enzymes, and other biological molecules are significantly affected because of their crowding. Thus, exploring the role of crowding environment on the denaturation and renaturation kinetics of protein molecules is of great importance. Here, CRABP I (cellular retinoic acid binding protein I) is employed as a model protein along with different molecular weights of Polyethylene glycol (PEG) as molecular crowders. The experimental evaluations are done by accessing the protein secondary structure analysis using circular dichroism (CD) spectroscopy and unfolding kinetics using intrinsic fluorescence of CRABP I at 37 °C to mimic the in vivo crowding environment. The unfolding kinetics results indicated that both PEG 2000 and PEG 4000 act as stabilizers by retarding the unfolding kinetic rates. Both kinetic and stability outcomes presented the importance of crowding environment on stability and kinetics of CRABP I. The molecular dynamics (MD) studies revealed that thirteen PEG 2000 molecules assembled during the 500 ns simulation, which increases the stability and percentage of β-sheet. The experimental findings are well supported by the molecular dynamics simulation results.

Effects of Ionic Liquids on Metalloproteins

In the past decade, innovative protein therapies and bio-similar industries have grown rapidly. Additionally, ionic liquids (ILs) have been an area of great interest and rapid development in industrial processes over a similar timeline. Therefore, there is a pressing need to understand the structure and function of proteins in novel environments with ILs. Understanding the short-term and long-term stability of protein molecules in IL formulations will be key to using ILs for protein technologies. Similarly, ILs have been investigated as part of therapeutic delivery systems and implicated in numerous studies in which ILs impact the activity and/or stability of protein molecules. Notably, many of the proteins used in industrial applications are involved in redox chemistry, and thus often contain metal ions or metal-associated cofactors. In this review article, we focus on the current understanding of protein structure-function relationship in the presence of ILs, specifically focusing on the effect of ILs on metal containing proteins.

Study on the interaction of polyamine transport (PAT) and 4-Chloro-naphthalimide-homospermidine conjugate (4-ClNAHSPD) by molecular docking and dynamics

Polyamine transporter (PAT) is a protein that can deliver "drug-polyamine" conjugates to tumor cells. 4-Chloro-naphthalimide- homospermidine (4-ClNAHSPD) displayed good antitumor activity and excellent cell selectivity via PAT pathway. In this paper, 4-ClNAHSPD and spermidine (SPD) were docked against PAT. The results showed that 4-ClNAHSPD could bind to PAT through hydrogen bond, Van der Waals, salt bridge or attractive charge and hydrophobic interaction. The interaction of SPD and PAT, however, was hydrogen bond and Van der Waals interaction. Moreover, their binding sites were also different. The primary binding sites of 4-ClNAHSPD with PAT are the residues of VAL59, HIS222, ASP61, ASP179 and GLU64, while SPD interacts with PAT in the sites of ASP37, ASP244, APS275 and SER36. The docked ligand-protein complexes were simulated for 5000ps. In simulations, various binding sites further resulted in the diverse root-mean-square deviation (RMSD) and root-mean-square deviation fluctuation (RMSF) values. The RMSD and RMSF values of 4-ClNAHSPD-PAT indicated that 4-ClNAHSPD caused a weak conformational change of PAT in a different style from SPD. More importantly, the interaction force numbers of 4-ClNAHSPD-PAT were also changed after the simulation. These results supported that 4-ClNAHSPD harnesses PAT pathway for cellular entrance.Communicated by Ramaswamy H. Sarma.

Investigation of the interaction of a polyamine-modified flavonoid with bovine serum albumin (BSA) by spectroscopic methods and molecular simulation

The interaction between BSA and compound 1 was studied by UV-vis, fluorescence and circular dichroism spectroscopy under physiological conditions (pH = 7.4). Molecular docking and molecular dynamics analyses were also performed. The results showed that compound 1 could bind to BSA. When compound 1 bound to BSA, there were a series of changes in the spectral properties of BSA, which were an enhancement effect of the UV-Vis spectrum of BSA, fluorescence quenching and a weak conformational change in the CD spectrum. The results of the fluorescence experiments at 298, 303 and 310 K showed that fluorescence quenching caused by the addition of compound 1 to BSA was generally static quenching accompanied by a dynamic quenching process, which was shown by the quenching constants of 2.010 × 10⁴ L∙M^-1, 1.850 × 10⁴ L∙M^-1, and 1.970 × 10⁴ L∙M^-1 at the three different temperatures, respectively. From the obtained binding constants and thermodynamic parameters, it was found that hydrophobic forces played an important role in the binding process of 1 to BSA. The results of synchronous fluorescence and three-dimensional fluorescence showed that compound 1 caused a weak conformational change in BSA. Docking results showed that compound 1 was located at binding site II of bovine serum albumin protease. In addition, the flavonoid moiety of compound 1 contributes to the hydrophobic binding of compound 1 to BSA. The results of molecular dynamics, including the root-mean-square deviation (RMSD) and RMS fluctuation (RMSF) values, showed that the binding of compound 1 to BSA did not cause a significant conformational change in BSA.

Microscopic Understanding of the Effect of Ionic Liquid on Protein from Molecular Simulation Studies

We have performed molecular dynamics (MD) simulations of the protein α-lactalbumin in aqueous solution containing the ionic liquid (IL) 1-butyl-3-methyl imidazolium tetrafluoroborate ([BMIM][BF₄]) as the cosolvent at different concentrations. Attempts have been made to obtain quantitative understanding of the effects of the IL on the conformational features of the protein as well as the distributions of the IL and water around it. The calculations revealed enhanced rigidity of the protein with reduced conformational fluctuations and increasingly correlated local motions in the presence of the IL. Nonuniform relative population of the BMIM⁺ and BF₄^- ions at the protein surface with respect to that in the bulk solution has been observed. It is demonstrated that exchange of water by the IL around the protein results in rearrangement of the hydrogen bond network at the interface with breaking of protein-water hydrogen bonds and formation of protein-IL hydrogen bonds. Importantly, it is found that the protein forms increased number of stronger salt bridges in the presence of IL. This shows that the formation of a greater number of such stronger salt bridges is the origin behind the enhanced rigidity of the protein in the presence of the IL.

A novel amalgamation of deep eutectic solvents and crowders as biocompatible solvent media for enhanced structural and thermal stability of bovine serum albumin

This study unravels the effect of a novel solvent medium designed by amalgamation of macromolecular crowders and deep eutectic solvents (DESs) on bovine serum albumin (BSA).

Molecular interactions of MnO2@RGO (manganese dioxide-reduced graphene oxide) nanocomposites with bovine serum albumin

Graphene based materials have attracted global attention due to their excellent properties. GO-metal oxide nanocomposites have been conjugated with biomolecules for the development of novel materials and potentially used as biomarkers. Herein, a detailed study on the interaction of Bovine serum albumin (BSA) with MnO₂@RGO (manganese dioxide-reduced graphene oxide) nanocomposites (NC) has been carried out. MnO₂@RGO nanocomposites were prepared through a template/surfactant free hydrothermal route at 180 °C for 12 h by varying the graphene oxide (GO) concentration. Different biophysical experiments have been carried out to evaluate molecular interactions between BSA and NCs. Intrinsic fluorescence has been used to quantify the quenching efficiency of NCs and the binding association of BSA-NC complexes. NCs effectively quenched the intrinsic fluorescence of BSA via static and dynamic mechanism. Further, the results indicate that the molecular interactions of NC with BSA are dependent on the GO percentage in NC. Circular dichroism results demonstrate nominal changes in the secondary structure of BSA in presence of NCs. Also, the esterase-like activity of BSA was marginally affected after adsorption upon NCs. In addition, the FESEM micrographs reveal that the protein-NC complexes consist of nanorod and sheet-like morphologies are forming aggregates of different sizes. We hope that this study will provide a basis for the design of novel graphene based and other related nanomaterials for several biological applications.Communicated by Ramaswamy H. Sarma.

Experimental and theoretical investigations on the interaction of l-methionine molecules with α-chymotrypsin in the aqueous solution using various methods

l-Methionine (l-Met) is one of the necessary amino acids that play unparalleled roles, influencing both the protein structure and metabolism. Understanding the interactions between proteins and small molecules can be realized by various perspectives, and this is significant for the progression of basic sciences and drug development. In this study, the variations in the stability, function, and structure of α-Chymotrypsin (α-Chy) in the presence of l-Met were investigated using spectroscopic and computational approaches. The results of the UV-vis absorption demonstrated that α-Chy had a maximum peak at 280 nm due to the Trp residue. Hyperchromism shift was seen in the presence of l-Met. Ground state system was formed in the presence of l-Met, as confirmed by the fluorescence studies. Fluorescence variations also revealed static quenching. The CD spectra also represented the alteration of the enzyme with an increase in the α-helix and a decrease in the β-sheet. The activity of α-Chy was incremented in the presence of l-Met. Therefore, l-Met served as an activator. Molecular docking results also indicated a negative amount for the Gibbs free energy of the binding of l-Met to the enzyme. α-Chy became more stable in the presence of l-Met, based on the molecular dynamics simulation.

Gallic acid influence on bovine serum albumin thermal stability

A thermoanalytical approach reveals the dual action of GA on BSA thermal stability.

Binding and inhibitory effect of the food colorants Sunset Yellow and Ponceau 4R on amyloid fibrillation of lysozyme

Amyloid fibrillogenesis of proteins is known to be the root cause of a large number of diseases like Parkinson's, Alzheimer's, and Huntington's disease, spongiform encephalopathy, amyloid polyneuropathy, type-II diabetes, etc.