Exploring the Counteracting Mechanism of Trehalose on Urea Conferred Protein Denaturation: A Molecular Dynamics Simulation Study

Efficient dissolution of cellulose in slow-cooling alkaline systems and interacting modes between alkali and urea at the molecular level

The dissolution of microcrystalline cellulose (MCC) in a urea-NaOH system is beneficial for its mechanical processing. The apparent MCC solubility was greatly improved to 14 wt% under a slow-cooling condition with a cooling rate of -0.3 °C/min. The cooling curve or thermal history played a crucial role in the dissolution process. An exotherm (-54.7 ± 3 J/g MCC) was detected by DSC only under the slow-cooling condition, and the cryogenic dissolution of MCC was attributed to the exothermic interaction between MCC and solvent. More importantly, the low cooling rate promoted the dissolution of MCC by providing enough time for the diffusion of OH- and urea into MCC granules at higher temperatures. The Raman spectral data showed that the intramolecularly and intermolecularly hydrogen bonds in cellulose were cleaved by NaOH and urea, respectively. XPS and solid-state 13C NMR results showed that hydrogen bonds were generated after dissolution, and a dual-hydrogen-bond binding mode between urea and cellulose was confirmed by DFT calculations. Both the decrease of enthalpy and increase of entropy dominated the spontaneity of MCC dissolution, and that is the reason for the indispensability of cryogenic environment. The high apparent solubility of MCC in the slow-cooling process and the dissolution mechanism are beneficial for the studies on cellulose modification and mechanical processing.

Molecular insights into the urea-choline-O-sulfate interactions in aqueous solution

Urea and choline-O-sulfate (COS) are both osmolytes, but have opposite effects on protein structure. Urea has been well-known for years to destabilize protein structure. Though COS has been revealed as an osmoprotective molecule against urea induced denaturation of proteins, the mechanism of this compensation is still unexplored. This study focuses on a theoretical investigation of the interdependent behavior of urea and COS in a mixture, to explore how urea becomes a weaker denaturing agent in the presence of COS. In this study, we have considered every possible interaction among the solute (urea and COS) and solvent (water) both at room temperature and high temperature, employing two different force field parameters i.e., CHARMM General Force Field parameters (CGenFF) and General AMBER Force Field (GAFF) parameters through classical molecular dynamics simulation studies. Different techniques have been used to analyze the average interactions between COS and urea as well as their solvation properties, which show that in the presence of COS, urea becomes a less effective denaturant than when alone. The water-water interaction shows that the mixed osmolyte solution of urea and COS strengthens the water hydrogen bonding network. The enhanced solvation of urea and COS in the urea-COS mixture and their mutual interactions, results in the exclusion of free urea as well as COS from the solution. This synergistic behavior of urea and COS could be the major reason behind COS counteracting urea's denaturation of proteins.

Interactions in Ternary Aqueous Solutions of NMA and Osmolytes-PARAFAC Decomposition of FTIR Spectra Series

Intermolecular interactions in aqueous solutions are crucial for virtually all processes in living cells. ATR-FTIR spectroscopy is a technique that allows changes caused by many types of such interactions to be registered; however, binary solutions are sometimes difficult to solve in these terms, while ternary solutions are even more difficult. Here, we present a method of data pretreatment that facilitates the use of the Parallel Factor Analysis (PARAFAC) decomposition of ternary solution spectra into parts that are easier to analyze. Systems of the NMA–water–osmolyte-type were used to test the method and to elucidate information on the interactions between N-Methylacetamide (NMA, a simple peptide model) with stabilizing (trimethylamine N-oxide, glycine, glycine betaine) and destabilizing osmolytes (n-butylurea and tetramethylurea). Systems that contain stabilizers change their vibrational structure to a lesser extent than those with denaturants. Changes in the latter are strong and can be related to the formation of direct NMA–destabilizer interactions.

Solvation energetics of proteins and their aggregates analyzed by all-atom molecular dynamics simulations and the energy-representation theory of solvation

Solvation is a controlling factor for the structure and function of proteins. This article addresses the effects of solvation from an energetic perspective for the fluctuations and cosolvent-induced changes in protein structures and the equilibrium of aggregate formation for a peptide. A theoretical framework to analyze the solvation effects with an explicit solvent is introduced by adopting the energy-representation theory of solvation, and the connection of the solvation free energy to the protein structure and the aggregation tendency is quantitatively described in combination with all-atom molecular dynamics simulations. The interaction components that govern the solvation effects on the structural variations of proteins are further identified through correlation analysis, and a computational scheme to assess the shift of an aggregation equilibrium due to the addition of a cosolvent is provided.

Understanding The Role of Reline, a Natural DES, on Temperature-Induced Conformational Changes of C-Kit G-Quadruplex DNA: A Molecular Dynamics Study

The noncanonical guanine-rich DNAs have drawn particular attention to the scientific world due to their controllable diverse and polymorphic structures. Apart from biological and medical significance, G-quadruplex DNAs are widely used in various fields such as nanotechnology, nanomachine, biosensors, and biocatalyst. So far, the applications of the G-quadruplex DNA are mainly limited in the water medium. Recently, a new generation of solvent named deep eutectic solvent (DES) has become very popular and has been widely used as a reaction medium of biocatalytic reactions and long-term storage medium for nucleic acids, even at high temperature. Hence, it is essential to understand the role of DES on temperature-induced conformational changes of a G-quadruplex DNA. In this research work, we have explored the temperature-mediated conformational dynamics of c-kit oncogene promoter G-quadruplex DNA in reline medium in the temperature range of 300-500 K, using a total of 10 μs unbiased all-atom molecular dynamics simulation. Here, from RMSD, RMSF, R_g and principal component analyses, we notice that the c-kit G-quadruplex DNA is stable up to 450 K in reline medium. However, it unfolds in water medium at 450 K. It is found that the hydrogen bonding interactions between c-kit G-quadruplex DNA and reline play a key role in the stabilization of the G-quadruplex DNA even at high temperature. Furthermore, in this work we have observed a very interesting and distinctive phenomenon of the central cation of the G-quadruplex DNA. Its position was seen to fluctuate between the two tetrad cores, that is, the region between tetrad-1 and tetrad-2 and that between tetrad-2 and tetrad-3 and vice versa at 450 and 500 K in reline medium which is absent in water medium at 450 K. Moreover, the rate of its oscillation is increased when temperature is increased.

ATP Controls the Aggregation of Aβ16-22 Peptides

The oligomerization of Aβ_16-22 peptide, which is the hydrophobic core region of full-length Aβ_1-42, causes Alzheimer's disease (AD). This progressive neurodegenerative disease affects over 44 million people worldwide. However, very few synthesized drug molecules are available to inhibit the aggregation of Aβ. Recently, experimental studies have shown that the biological ATP molecule prevents Aβ fibrillation at the millimolar scale; however, the significance of ATP molecules on Aβ fibrillation and the mechanism behind it remain elusive. We have carried out a total of 7.5 μs extensive all-atom molecular dynamics and 8.82 μs of umbrella sampling in explicit water using AMBER14SB, AMBER99SB-ILDN, and AMBER-FB15 force fields for Aβ_16-22 peptide, to investigate the role of ATP on the disruption of Aβ_16-22 prefibrils. From various analyses, such as secondary structure analysis, residue-wise contact map, SASA, and interaction energies, we have observed that, in the presence of ATP, the aggregation of Aβ_16-22 peptide is very unfavorable. Moreover, the biological molecule ATP interacts with the Aβ_16-22 peptide via hydrogen bonding, π-π stacking, and NH-π interactions which, ultimately, prevent the aggregation of Aβ_16-22 peptide. Hence, we assume that the deficiency of ATP may cause Alzheimer's disease (AD).

Efficacy of several additives to modulate the phase behavior of biomedical polymers: A comprehensive and comparative outlook

Several new classes of polymeric materials are being introduced with unique properties. Thermoresponsive polymers (TRPs) are one of the most fascinating and emerging class of biomaterials in biomedical research. The design of TRPs with good response to temperature and its ability to exhibit coil to globular transition behavior near to physiological temperature made them more promising materials in the field of biomaterials and biomedicines. Instead of numerous studies on TRPs, the mechanistic interplay among several additives and TRPs is still not understood clearly and completely. The lack of complete understanding of biomolecular interactions of various additives with TRPs is limiting their applications in interdisciplinary science as well as pharmaceutical industry. There is a great need to provide a collective and comprehensive information of various additives and their behavior on widely accepted biopolymers, TRPs such as poly(N-isopropylacrylamide) (PNIPAM), poly(vinyl methyl ether) (PVME), poly(N-vinylcaprolactum) (PVCL) and poly(ethylene glycol)-poly(propylene glycol)-poly(ethylene glycol) (PEG-PPG-PEG) in aqueous solution. Obviously, as the literature on the influence of various additives on TRPs is very vast, therefore we focus our review only on these four selected TRPs. Additives such as polyols, methylamines, surfactants and denaturants basically made the significant changes in water structure associated to polymer via their entropy variation which is the direct influence of their directly or indirectly binding abilities. Eventually, this review addresses a brief overview of the most recent literature of applications based phase behavior of four selected TRPs in response to external stimuli. The work enhances the knowledge for use of TRPs in the advanced development of drug delivery system and in many more pharmaceutical applications. These kinds of studies provide powerful impact in exploring the utility range of polymeric materials in various field of science.

Effect of Osmolytes on Conformational Behavior of Intrinsically Disordered Protein α-Synuclein

α-Synuclein is an intrinsically disordered protein whose function in a healthy brain is poorly understood. It is genetically and neuropathologically linked to Parkinson's disease (PD). PD is manifested after the accumulation of plaques of α-synuclein aggregates in the brain cells. Aggregates of α-synuclein are very toxic and lead to the disruption of cellular homeostasis and neuronal death. α-Synuclein can also contribute to disease propagation as it may exert noxious effects on neighboring cells. Understanding the mechanism of α-synuclein aggregation will facilitate the problem of dealing with neurodegenerative diseases in general and that of PD in particular. Here, we have used molecular dynamics simulations to investigate the behavior of α-synuclein at various temperatures and in different concentrations of urea and trimethyl amine oxide. The residue region from 61 to 95 of α-synuclein is experimentally known as amyloidogenic. In our study, we have identified some other regions, which also have the propensity to form an aggregate besides this known sequence. Urea being a denaturant interacts more with these regions of α-synuclein through hydrogen bond formation and inhibits the β-sheet formation, whereas trimethyl amine oxide itself does not interact much with the protein and stabilizes the protein by preferentially distributing water molecules on the surface of the protein.

Exploring Dynamics and Structure of Biomolecules, Cryoprotectants, and Water Using Molecular Dynamics Simulations: Implications for Biostabilization and Biopreservation

Successful stabilization and preservation of biological materials often utilize low temperatures and dehydration to arrest molecular motion. Cryoprotectants are routinely employed to help the biological entities survive the physicochemical and mechanical stresses induced by cold or dryness. Molecular interactions between biomolecules, cryoprotectants, and water fundamentally determine the outcomes of preservation. The optimization of assays using the empirical approach is often limited in structural and temporal resolution, whereas classical molecular dynamics simulations can provide a cost-effective glimpse into the atomic-level structure and interaction of individual molecules that dictate macroscopic behavior. Computational research on biomolecules, cryoprotectants, and water has provided invaluable insights into the development of new cryoprotectants and the optimization of preservation methods. We describe the rapidly evolving state of the art of molecular simulations of these complex systems, summarize the molecular-scale protective and stabilizing mechanisms, and discuss the challenges that motivate continued innovation in this field.

Can an ammonium-based room temperature ionic liquid counteract the urea-induced denaturation of a small peptide?

The folding/unfolding equilibrium of proteins in aqueous medium can be altered by adding small organic molecules generally termed as co-solvents.

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.

Free-energy analysis of protein solvation with all-atom molecular dynamics simulation combined with a theory of solutions

The structure of a protein is strongly influenced by solvation. In the present review, the solvation effect is treated within the framework of statistical thermodynamics. The key quantity is the solvation free energy of protein and a fast method for its computation with explicit solvent is introduced. The applications of the method to the structural fluctuation of protein in water, structure determination of protein-protein complex, and urea effect on protein structure are then described, and the roles of solvent water and cosolvent are discussed from the standpoint of energetics.

Molecular basis for competitive solvation of the Burkholderia cepacia lipase by sorbitol and urea

The molecular scale diversity of protein–solvent interactions.