Abdul Rajjak Shaikh

Effects of arginine on heat-induced aggregation of concentrated protein solutions

Arginine is one of the commonly used additives to enhance refolding yield of proteins, to suppress aggregation of proteins, and to increase solubility of proteins, and yet the molecular interactions that contribute to the role of arginine are unclear. Here, we present experiments, using bovine serum albumin (BSA), lysozyme (LYZ), and β‐lactoglobulin (BLG) as model proteins, to show that arginine can enhance heat‐induced aggregation of concentrated protein solutions, contrary to the conventional belief that arginine is a universal suppressor of aggregation. Results show that the enhancement in aggregation is caused only for BSA and BLG, but not for LYZ, indicating that arginines preferential interactions with certain residues over others could determine the effect of the additive on aggregation. We use this previously unrecognized behavior of arginine, in combination with density functional theory calculations, to identify the molecular‐level interactions of arginine with various residues that determine arginines role as an enhancer or suppressor of aggregation of proteins. The experimental and computational results suggest that the guanidinium group of arginine promotes aggregation through the hydrogen‐bond‐based bridging interactions with the acidic residues of a protein, whereas the binding of the guanidinium group to aromatic residues (aggregation‐prone) contributes to the stability and solubilization of the proteins. The approach, we describe here, can be used to select suitable additives to stabilize a protein solution at high concentrations based on an analysis of the amino acid content of the protein.

Arginine-aromatic interactions and their effects on arginine-induced solubilization of aromatic solutes and suppression of protein aggregation.

We examine the interaction of aromatic residues of proteins with arginine, an additive commonly used to suppress protein aggregation, using experiments and molecular dynamics simulations. An aromatic‐rich peptide, FFYTP (a segment of insulin), and lysozyme and insulin are used as model systems. Mass spectrometry shows that arginine increases the solubility of FFYTP by binding to the peptide, with the simulations revealing the predominant association of arginine to be with the aromatic residues. The calculations further show a positive preferential interaction coefficient, ΓXP, contrary to conventional thinking that positive ΓXPs indicate aggregation rather than suppression of aggregation. Simulations with lysozyme and insulin also show arginines preference for aromatic residues, in addition to acidic residues. We use these observations and earlier results reported by us and others to discuss the possible implications of arginines interactions with aromatic residues on the solubilization of aromatic moieties and proteins. Our results also highlight the fact that explanations based purely on ΓXP, which measures average affinity of an additive to a protein, could obscure or misinterpret the underlying molecular mechanisms behind additive‐induced suppression of protein aggregation.

Effects of Water Concentration on the Free Volume of Amino Acid Ionic Liquids Investigated by Molecular Dynamics Simulations

Amino acid ionic liquids (AAILs) are gaining attention because of their potential in CO2 capture technology. Molecular dynamics simulations of AAILs tetramethylammonium glycinate ([N1111][Gly]), tetrabutylammonium glycinate ([N4444][Gly]), and 1,1,1-trimethylhydrazinium glycinate ([aN111][Gly]) and their corresponding mixtures with water were performed to investigate the effect of water concentration on the cation-anion interactions. The water content significantly influenced the free volume (FV) and fractional free volume (FFV) of the AAILs that varied with the hydrophobic and hydrophilic nature of the ion pairs. Under dry conditions, the FFV increased with increasing cation molecular sizes, indicative of proportional adsorption of any inert gases, such as N2, as consistent with experimental observations. Furthermore, the polarity of the cation played an important role in FFV and hence the diffusion of the AAILs. Density functional theory calculations suggested that hydrophilic [aN111][Gly] featured stronger interactions in the presence of water, whereas the hydrophobic IL showed weaker interactions. The carboxylate group of glycinate displayed stronger interactions with water than the cation. The computational study provided qualitative insight into the role of FV of the AAILs on CO2 and N2 absorption and suggests that [aN111][Gly] has CO2 adsorption capacity in the presence of water superior to that of other studied AAILs.

Quantum chemical studies for oxidation of morpholine by Cytochrome P450

Since morpholine oxidation has recently been shown to involve Cytochrome P450, the study on its mechanism at molecular level using quantum chemical calculations for the model of cytochrome active site is reported here. The reaction pathway is investigated for two electronic states, the doublet and the quartet, by means of density functional theory. The results show that morpholine hydroxylation occurs through hydrogen atom abstraction and rebound mechanism. However, in the low spin state, the reaction is concerted and hydrogen atom abstraction yields directly ferric-hydroxy morpholine complex without a distinct rebound step while in quartet state the reaction is stepwise. The presence of nitrogen in a morpholine heterocycle is postulated to greatly facilitate hydrogen abstraction. The hydroxylated product undergoes intramolecular hydrogen atom transfer from hydroxy group to nitrogen, leading to the cleavage of the C-N bond and the formation of 2-(2-aminoethoxy) acetaldehyde. The cleavage of the C-N bond is indicated as the rate-determining step for the studied reaction. The assistance of explicit water molecule is shown to lower the energy barrier for the C-N bond cleavage in enzymatic environment whereas solvent effects mimicked by COSMO solvent model have minor influence on relative energies along the pathway.

Interaction of arginine, lysine, and guanidine with surface residues of lysozyme: implication to protein stability

Additives are widely used to suppress aggregation of therapeutic proteins. However, the molecular mechanisms of effect of additives to stabilize proteins are still unclear. To understand this, we herein perform molecular dynamics simulations of lysozyme in the presence of three commonly used additives: arginine, lysine, and guanidine. These additives have different effects on stability of proteins and have different structures with some similarities; arginine and lysine have aliphatic side chain, while arginine has a guanidinium group. We analyze atomic contact frequencies to study the interactions of the additives with individual residues of lysozyme. Contact coefficient, quantified from contact frequencies, is helpful in analyzing the interactions with the guanidine groups as well as aliphatic side chains of arginine and lysine. Strong preference for contacts to the additives (over water) is seen for the acidic followed by polar and the aromatic residues. Further analysis suggests that the hydration layer around the protein surface is depleted more in the presence of arginine, followed by lysine and guanidine. Molecular dynamics simulations also reveal that the internal dynamics of protein, as indicated by the lifetimes of the hydrogen bonds within the protein, changes depending on the additives. Particularly, we note that the side-chain hydrogen-bonding patterns within the protein differ with the additives, with several side-chain hydrogen bonds missing in the presence of guanidine. These results collectively indicate that the aliphatic chain of arginine and lysine plays a critical role in the stabilization of the protein.

Dynamic and structural changes in the minimally restructuring EcoRI Bound to a minimally mutated DNA chain.

Abstract The dynamics of a protein plays an important role in protein functionality. Here, we examine the differences in the dynamics of a minimally restructuring protein, EcoRI, when it is bound to its cognate DNA and to a noncognate sequence which differs by just a single basepair. Molecular dynamics simulations of the complexes and essential dynamics analyses reveal that the overall dynamics of the protein subunits change from a coordinated motion in the cognate complex to a scrambled motion in the noncognate complex. This dynamical difference extends to the protein-DNA interface where EcoRI tries to constrict the DNA in the cognate complex. In the noncognate complex, absence of the constricting motion of interfacial residues, overall change in backbone dynamics and structural relaxation of the arms enfolding the DNA leave the DNA less-kinked relative to the situation in the cognate complex, thus indicating that the protein is poised for linear diffusion along the DNA rather than for catalytic action. In a larger context, the results imply that the DNA sequences dictate protein dynamics and that when a protein chances upon the recognition sequence some of the key domains of the protein undergo dynamical changes that prepare the protein for eventual catalytic action.

Adsorption of Bovine Serum Albumin on Poly(vinylidene fluoride) Surfaces in the Presence of Ions: A Molecular Dynamics Simulation

Adsorption of bovine serum albumin (BSA) on poly(vinylidene fluoride) (PVDF) surfaces in an aqueous environment was investigated in the presence and absence of excess ions using molecular dynamics simulations. The adsorption process involved diffusion of protein to the surface and dehydration of surface-protein interactions, followed by adsorption and denaturation. Although adsorption of BSA on PVDF surface was observed in the absence of excess ions, denaturation of BSA was not observed during the simulation (1 μs). Basic and acidic amino acids of BSA were found to be directly interacting with PVDF surface. Simulation in a 0.1 M NaCl solution showed delayed adsorption of BSA on PVDF surfaces in the presence of excess ions, with BSA not observed in close proximity to PVDF surface within 700 ns. Adsorption of Cl- on PVDF surface increased its negative charge, which repelled negatively charged BSA, thereby delaying the adsorption process. These results will be helpful for understanding membrane fouling phenomena in polymeric membranes, and fundamental advancements in these areas will lead to a new generation of membrane materials with improved antifouling properties and reduced energy demands.

Dual Superlyophobic Aliphatic Polyketone Membranes for Highly Efficient Emulsified Oil–Water Separation: Performance and Mechanism

Efficient treatment of difficult emulsified oil-water wastes is a global challenge. Membranes exhibiting unusual dual superlyophobicity (combined underwater superoleophobicity and underoil superhydrophobicity) are intriguing to realize high-efficiency separation of both oil-in-water and water-in-oil emulsions. For the first time, a robust polymeric membrane demonstrating dual superlyophobicity to common apolar oils was facilely fabricated via a simple one-step phase separation process using an aliphatic polyketone (PK) polymer, thanks to a conjunction of intermediate hydrophilicity and re-entrant fibril-like texture upon the prepared PK membrane. Further chemical modification to improve surface hydrophilicity slightly can enable dual superlyophobicity to both apolar and polar oils. It is found that a nonwetting composite state of oil against water or water against oil was obtainable on the membrane surfaces only when the probe liquids possess an equilibrium contact angle (θow or θwo) larger than the critical re-entrant angle of the textured surfaces (73°), which can explain the existences of dual superlyophobicity and also the nonwetting to fully wetting transitions. A simple design chart was developed to map out the operational windows of material hydrophilicity and re-entrant geometry, that is, a possible zone, to help in the rational design of similar interfacial systems from various materials. Switchable filtrations of oil-in-water and water-in-oil nanoemulsions were achieved readily with both high flux and high rejection. The simplicity and scalability of the membrane preparation process and the well-elucidated underlying mechanisms illuminate the great application potential of the PK-based superwetting membranes.

Model first principles molecular dynamics study on the fate of vibrationally excited states in liquid water

Carr–Parrinello MD calculations for a simplistic periodic model of liquid water are performed to probe temperature dependence of infrared activation lifetime. IR activation is classically simulated by adding an appropriate velocity to the proton in a tagged water molecule. The evolution of hydrogen bonding descriptors is monitored through consecutive simulations to spot the onset of qualitative changes in the hydrogen bonding network; they are related to vibrational energy relaxation. The applied ionic simulation temperature (elevated by 20%) decreases the tendency to overbinding characteristic for CP MD calculations. Qualitatively estimated stretch lifetimes are 280, 320 and 400 fs for temperatures of 298, 320 and 370 K, respectively. This work gives direct evidence of the parallel dependence of both the decay of OH activation and the hydrogen bond network on temperature, which offers a viable explanation for the experimentally observable unusual increase in OH excitation lifetime with temperature.